I would like to thank everybody for their help. We finally got everything up and running. What ended up happening was a series of unrelated events that caused only the compressor to stop working. First our pwm cables to the had been damaged and kept causing trouble. At this point it worked 50% of the time. After replacing these the compressor stopped working all together. This is when we started this post. All of a sudden it decides to work this morning (still don't know why?) after extensive testing with a multimeter but it wouldn't turn off!! Our code to regulate it didn't seem to work. After testing the pressure sensor we found that the pwm for it was plugged in but it wasn't getting power!
Well thats when we remembered that not all our pwms were long enough to reach the controller so instead of splicing them and soldering two together we had just connected them and taped them and the splice had come apart! After fixing that and reinstalling our original code we finally got it to work properly.
In summery Ive learned two things. One: make sure everyone next year knows the proper way to wire (and make sure were super neat). Two: I REALLY hate pneumatics!