Issues Aligning ATC in both x and y axes on pcnc440

So my community college makerspace has a PCNC440 that supposedly nobody has used in 2 years. I had experience machining in high school on haas machines, so I was pretty happy to see there was a cnc machine at the college. Unfortunately, the ATC was misaligned so Ive been trying to fix it, however I am having some issues.

The main problem is that the tool tray is misaligned in the Y axis, so I loosened the Adjustable nuts on the back. This starts to align it, however once it gets aligned, the ATC starts hitting the z axis head.

The ATC’s jam nut and coupler are already maxed out in the leftmost position, so I cannot get it any further away from the spindle without misaligning it again in the Y axis. Ive been following the manual I have on hand, but I cant find anything in there regarding aligning the atc in the Y axis, so I’ve been following this video: https://www.youtube.com/watch?v=HNNd7KiZ6eA&t=630s

Any thoughts on how I can align both the X and Y axis? I have not touched the fixed nut since I never saw anything telling me to touch it.

It’s been over a year since i installed an ATC on a 440 so i can’t offer much. However, this looks like a perfect scenario to reach out to our support department. Tormach.com>Support

The one on the pneumatic? You don’t see threads? I currently see several threads on mine where it’s pretty close to aligned but I have an early revision 440 and ATC.

You probably need to take a breather and go back to the beginning and look at the main bolt adjustment and sadly, I would go through the whole instructions and confirm it was installed/assembled correctly…who knows what has been done to it in that sort of environment…maybe a good time to get a 3-ring binder and create a maintenance log while you are at it…

…and contact support so you can make chips…without manual tool changes…which is always an option if you have something you need to do ASAP…

This looks like a case of (someone that thought they knew what they were doing found a box of equipment (the tool changer) and installed it. Unfortunately they just bolted it up and said done.) if I were you I would check every instruction as the tool changer is very finicky and any mid steps can cause headaches forever. Probably a uninstall and reinstall job.