I've been trying to upload the firmware via AVRDUDE.
The following is a snippet of what happens when I run AVRDUDE with the following:
" avrdude -C[path]/avrdude.conf -v -v -v -v -patmega1280 -cstk500 -Pcom3 -b57600 -D -Uflash:w:[firmware .hex file]:i "


Code:
                                  Block Poll               Page      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  Max
W   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ---
-- ---------
           efuse          0     0     0    0 no          1    0      0  9000  90
00 0x00 0x00
             Memory Ops:
               Oeration     Inst Bit  Bit Type  Bitno  Value
               -----------  --------  --------  -----  -----
               READ               31     VALUE      7      0
                                  30     VALUE      6      1
                                  29     VALUE      5      0
                                  28     VALUE      4      1
                                  27     VALUE      3      0
                                  26     VALUE      2      0
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23     VALUE      7      0
                                  22     VALUE      6      0
                                  21     VALUE      5      0
                                  20     VALUE      4      0
                                  19     VALUE      3      1
                                  18     VALUE      2      0
                                  17     VALUE      1      0
                                  16     VALUE      0      0
                                  15    IGNORE      7      0
                                  14    IGNORE      6      0
                                  13    IGNORE      5      0
                                  12    IGNORE      4      0
                                  11    IGNORE      3      0
                                  10    IGNORE      2      0
                                   9    IGNORE      1      0
                                   8    IGNORE      0      0
                                   7    OUTPUT      7      0
                                   6    OUTPUT      6      0
                                   5    OUTPUT      5      0
                                   4    OUTPUT      4      0
                                   3    OUTPUT      3      0
                                   2    OUTPUT      2      0
                                   1    OUTPUT      1      0
                                   0    OUTPUT      0      0
               WRITE              31     VALUE      7      1
                                  30     VALUE      6      0
                                  29     VALUE      5      1
                                  28     VALUE      4      0
                                  27     VALUE      3      1
                                  26     VALUE      2      1
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23     VALUE      7      1
                                  22     VALUE      6      0
                                  21     VALUE      5      1
                                  20     VALUE      4      0
                                  19     VALUE      3      0
                                  18     VALUE      2      1
                                  17     VALUE      1      0
                                  16     VALUE      0      0
                                  15    IGNORE      7      0
                                  14    IGNORE      6      0
                                  13    IGNORE      5      0
                                  12    IGNORE      4      0
                                  11    IGNORE      3      0
                                  10    IGNORE      2      0
                                   9    IGNORE      1      0
                                   8    IGNORE      0      0
                                   7    IGNORE      7      0
                                   6    IGNORE      6      0
                                   5    IGNORE      5      0
                                   4    IGNORE      4      0
                                   3    IGNORE      3      0
                                   2     INPUT      2      0
                                   1     INPUT      1      0
                                   0     INPUT      0      0
                                  Block Poll               Page
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  Max
W   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ---
-- ---------
           lock           0     0     0    0 no          1    0      0  9000  90
00 0x00 0x00
             Memory Ops:
               Oeration     Inst Bit  Bit Type  Bitno  Value
               -----------  --------  --------  -----  -----
               READ               31     VALUE      7      0
                                  30     VALUE      6      1
                                  29     VALUE      5      0
                                  28     VALUE      4      1
                                  27     VALUE      3      1
                                  26     VALUE      2      0
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23     VALUE      7      0
                                  22     VALUE      6      0
                                  21     VALUE      5      0
                                  20     VALUE      4      0
                                  19     VALUE      3      0
                                  18     VALUE      2      0
                                  17     VALUE      1      0
                                  16     VALUE      0      0
                                  15    IGNORE      7      0
                                  14    IGNORE      6      0
                                  13    IGNORE      5      0
                                  12    IGNORE      4      0
                                  11    IGNORE      3      0
                                  10    IGNORE      2      0
                                   9    IGNORE      1      0
                                   8    IGNORE      0      0
                                   7    IGNORE      7      0
                                   6    IGNORE      6      0
                                   5    OUTPUT      5      0
                                   4    OUTPUT      4      0
                                   3    OUTPUT      3      0
                                   2    OUTPUT      2      0
                                   1    OUTPUT      1      0
                                   0    OUTPUT      0      0
               WRITE              31     VALUE      7      1
                                  30     VALUE      6      0
                                  29     VALUE      5      1
                                  28     VALUE      4      0
                                  27     VALUE      3      1
                                  26     VALUE      2      1
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23     VALUE      7      1
                                  22     VALUE      6      1
                                  21     VALUE      5      1
                                  20    IGNORE      4      0
                                  19    IGNORE      3      0
                                  18    IGNORE      2      0
                                  17    IGNORE      1      0
                                  16    IGNORE      0      0
                                  15    IGNORE      7      0
                                  14    IGNORE      6      0
                                  13    IGNORE      5      0
                                  12    IGNORE      4      0
                                  11    IGNORE      3      0
                                  10    IGNORE      2      0
                                   9    IGNORE      1      0
                                   8    IGNORE      0      0
                                   7     VALUE      7      1
                                   6     VALUE      6      1
                                   5     INPUT      5      0
                                   4     INPUT      4      0
                                   3     INPUT      3      0
                                   2     INPUT      2      0
                                   1     INPUT      1      0
                                   0     INPUT      0      0
                                  Block Poll               Page
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  Max
W   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ---
-- ---------
           calibration    0     0     0    0 no          1    0      0     0
 0 0x00 0x00
             Memory Ops:
               Oeration     Inst Bit  Bit Type  Bitno  Value
               -----------  --------  --------  -----  -----
               READ               31     VALUE      7      0
                                  30     VALUE      6      0
                                  29     VALUE      5      1
                                  28     VALUE      4      1
                                  27     VALUE      3      1
                                  26     VALUE      2      0
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23    IGNORE      7      0
                                  22    IGNORE      6      0
                                  21    IGNORE      5      0
                                  20    IGNORE      4      0
                                  19    IGNORE      3      0
                                  18    IGNORE      2      0
                                  17    IGNORE      1      0
                                  16    IGNORE      0      0
                                  15     VALUE      7      0
                                  14     VALUE      6      0
                                  13     VALUE      5      0
                                  12     VALUE      4      0
                                  11     VALUE      3      0
                                  10     VALUE      2      0
                                   9     VALUE      1      0
                                   8     VALUE      0      0
                                   7    OUTPUT      7      0
                                   6    OUTPUT      6      0
                                   5    OUTPUT      5      0
                                   4    OUTPUT      4      0
                                   3    OUTPUT      3      0
                                   2    OUTPUT      2      0
                                   1    OUTPUT      1      0
                                   0    OUTPUT      0      0
                                  Block Poll               Page
      Polled
           Memory Type Mode Delay Size  Indx Paged  Size   Size #Pages MinW  Max
W   ReadBack
           ----------- ---- ----- ----- ---- ------ ------ ---- ------ ----- ---
-- ---------
           signature      0     0     0    0 no          3    0      0     0
 0 0x00 0x00
             Memory Ops:
               Oeration     Inst Bit  Bit Type  Bitno  Value
               -----------  --------  --------  -----  -----
               READ               31     VALUE      7      0
                                  30     VALUE      6      0
                                  29     VALUE      5      1
                                  28     VALUE      4      1
                                  27     VALUE      3      0
                                  26     VALUE      2      0
                                  25     VALUE      1      0
                                  24     VALUE      0      0
                                  23    IGNORE      7      0
                                  22    IGNORE      6      0
                                  21    IGNORE      5      0
                                  20    IGNORE      4      0
                                  19    IGNORE      3      0
                                  18    IGNORE      2      0
                                  17    IGNORE      1      0
                                  16    IGNORE      0      0
                                  15    IGNORE      7      0
                                  14    IGNORE      6      0
                                  13    IGNORE      5      0
                                  12    IGNORE      4      0
                                  11    IGNORE      3      0
                                  10    IGNORE      2      0
                                   9   ADDRESS      1      0
                                   8   ADDRESS      0      0
                                   7    OUTPUT      7      0
                                   6    OUTPUT      6      0
                                   5    OUTPUT      5      0
                                   4    OUTPUT      4      0
                                   3    OUTPUT      3      0
                                   2    OUTPUT      2      0
                                   1    OUTPUT      1      0
                                   0    OUTPUT      0      0


         Programmer Type : STK500V2
         Description     : Atmel STK500 Version 2.x firmware
         Programmer Model: Unknown
avrdude: Send: . [1b] . [01] . [00] . [02] . [0e] . [03] . [90] . [85]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv:
avrdude: stk500v2_ReceiveMessage(): timeout
avrdude: Send: . [1b] . [01] . [00] . [01] . [0e] . [01] . [14]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
avrdude: Recv: . [d5]
avrdude: Recv: . [01]
avrdude: Recv: . [80]
avrdude: Recv: . [8c]
This was copied a minute or two after running the command mentioned above.
The sections that say "avrdude: Send:" and "avrdude: Recv:" over and over continue on for a while with intermittent "out of sync" or "failure to execute command" errors spliced in.
Eventually the program just stops and the firmware still hadn't taken.

It seems that AVRDUDE is starting to upload a file, but for some reason it times out before it can finish or something.
There is a green LED that flashes underneath the printer every time a new section of send and recv appears.
When I try other '-c' parameters (like arduino) I just get an "out of sync" error after about three sends that each have one recv.

I couldn't copy any more command prompt stuff since the whole "memory blocks" dump is longer than the command window.
Anything else was repetition mostly of what is seen above, anyways.