Ok, heres what I finally found out.
Z Problem - Someone had moved the router head, and the bit wasn't clearing to our spoilage board. A part of the machine itself was touching the wood before the bit could go through. Thats why our z was off by 2mm.
X and Y Hopefully - I checked another thread of someone having the same issue and saying that it was the E - Stop switches that were not wired correctly, or poorly wired. So we undid all of the cover plates for them and checked the wires. We found some pinched wires under some E - Tape that we think might have been the issue. We re-wired them and everything seems to work fine. It will take some time to tell if it did the trick. But for now we are operational.
Thank you for your help Hood.
Austin