Replicator 2X: All movement off by a factor of two

I am a complete noob with 3D printing and am starting to do work on a MakerBot Replicator 2X. The Mightyboard on this printer was fried by someone previously, and I am basically trying to get it back to operable. I am running Sailfish 7.7 and think that I have everything working except for one issue.

My printer moves two times the distance that it thinks that it does. For example, when I jog 10 mm using Simplify3D in any direction, the extruders/build plate move 20 mm. This is also an issue when I try to print anything because the printer tries to move to Simplify's default positions and it runs into the wall in the x and y directions. This makes the printer completely inoperable. Also, the pre-print simulation in Simplify shows the print occuring as it should, so I know that it is probably a firmware or steps-per-mm issue.

I've been looking around on forums pretty much everywhere and haven't found anything that is way too complicated for someone with no experience in this. I wanted to try using g-code and m-code commands in the Simplify interface, but it said that MakerBot only accepts binary inputs, so I can't fix it that way. If someone could help me out with this or give any suggestions, then that would be dope.

-Ben