So it turns out my Makerbot is just fine. Remember that build platform upgrade I did a few weeks back? The removable glass platforms that BottleWorks made are longer on one side, I have no idea why, because the only thing that happens with that is if you put it on wrong it blocks the Y-gantry, which is what I did. Jog mode worked fine because the Z-platform and it's obstruction was out of the way between prints.
Of course I didn't discover this until after I had flipped it over an inspected the motherboard connections. They're fine by the way.
So my bad, my printer is just fine, I'm back in business and my biggest problem now is making sure prints stick to the build platform. Thank goodness for that.