Looking for info about NBT55’s

So this past week I was sent to work on an NBT55 crane, and ran into a very weird issue and hoping someone with more experience with them or just Nationals in general can chime in. Anyways quick backstory, First complaint crane lost comm with the LMI, found the LMI module to be bad, replaced. was good for about a year. New complaint was swing brake pedal wasn't working, another tech diagnosed the output on the master module was dead, so customer ordered new master module preprogrammed to serial of crane. Once received installed new module and tested, swing brake pedal works but have lost throttle on the truck from the crane cab. truck still starts and shuts down from crane cab. I get there, hook up software and check values on throttle are being received and set proper. They're a little off but are working. I found the Eng select in the EEPROM to be set for the wrong engine, set value to engine of the truck no throttle. check the rest of the EEPROM for issues that would prevent throttle but none found. Decide to plug in old master to see if i still Have throttle with it and I do. So Reinstall new Master. When I reinstalled new Master some weird things started happening, a bunch of modules now show "In Stub" in the software but the canbus still shows OK, Also now with loss of throttle I've lost truck start from the crane cab. Decide to plug in the old module so the Crane can atleast go back to work in the yard, but the old Master is now replicating what the new one is, although i checked my voltage for swing brake and it's now supplying a voltage?! I'm quite confused any input is appreciated.