Mycenter-1 w/ Fanuc O-M parameter problems

Okay so here is a little background on my situation. I have a 1996 Kitamura Mycenter-1 with a Fanuc O-M controller that had been completely off power (not connected at all) for around 2 months. I got around to hooking it up this past weekend and my troubles began. I was greeted with alarm 100, 417, 427, and 437. All the 400 alarms said something about x,y, and z parameters having a problems. Alarm 100 was due to PWE being enabled. All modes were locked and it was in a state of THNDLE (not to be confused with HNDL) so I could not switch to MDI or any other mode. I concluded that the machine had lost its parameters. Luckily I had a paper copy of parameters n1-n1128, n2000-n2128, n3000-n3128, n8100-n8398. I was able to input these by hand. I turned off the PWE setting and restarted the machine. All the alarms disappeared and I was able to home the machine. I tried to run the spindle and I received alarm NO. 2017 SP. TIME OVER/ WARM-UP ALARM. When I went to do a tool change I received a T-CODE SELECT MISS. I talked to Kitamura customer support and a gentleman told me I needed to input some diagnostic parameters/timers as well. I found a copy of some diagnostic parameters which included timers and inputed them. I restarted the machine and was now able to run the spindle. However, when I tried to tool change the pin located on the pallet changer would not disengage the hook locking the pot. To be more clear the pallet would rotate to the specified tool and then it would engage and disengage the lock holding the pot very quickly and repeatedly until I either pressed e-stop (which would leave the pot locked) or hit the reset key (which would leave the pot unlocked). I went on the phone again with Kitamura and was told to fine adjust the pallet via the encoder found on the pallet as the pin that was supposed to unlock the pot was perhaps not entering smoothly. I did this but if I tuned it say for tool 1 it wouldn't work for any other tool or for tool 1 once the pallet came back to that tool. I put the encoder to the original position and did a tool change and hit reset to unlock the pot. I took over manually and brought the pot down and tried to get the arm to move but it hit the spindle slightly and got stuck (I have fixed this now). I also noticed that the spindle will not orient itself for a tool change. What am I missing? The z axis is slightly to low, to spindle won't orient itself correctly for a tool change, and the pot won't unlock and come forward. Am I missing parameters? Everything seems to be associated with tool changing. Any help would be appreciated. Thanks.