Printrbot Rev D board

I have a old printrbot Rev D board from my first 3D printer I bought years ago. I've built another printer, an I3 style one and would like to use this board on the new frame but I'm having some issues. When I use (Atmel Flip) the normal method of flashing the firmware to the printrboard I can get marlin on there but it leaves me with a couple issues. The Y endstop is always triggered, Aslo, I cant remember how to edit firmware on this board and couldnt find any thing online to help. If I could edit the firmware I could just fix the Y stop from being triggered.

I've also tried flashing marlin through the Arduino IDE using a few mods for at90usb1286 controllers. I followed all instructions to the T from this link: [blog.lincomatic.com] but still couldnt get my board to accept the firmware, this would have been really been beneficial sense I could have edited the firmware like a Ramps 1.4 board and use the config.h file.

Its been a few years since I've used this printrboard so I forgot exactly how it worked but I do remember it being a REAL PAIN compared to a ramps 1.4 but it does lay out nice prints when its working correctly.