UP-165 phantom R axis collisions

Hi so I bought 2 up-165s and 2 up-130s as a lot both up-130 systems are complete one of the up-165s has a wrecked cable set so I only have one working up-165. When I first was working with R1 of the up-165s it was working well until the R axis started to get collision errors when rotated with the B axis perpendicular to the forearm. R would get stuck perpendicular then I would have to release the R brake and set back in position with a crowbar. When I ran the arm with the wrist removed and spun R continuously with limits released the collision would not occur, thus I thought the issue was a bad wrist bearing or a chipped tooth or something. I rebuilt the wrist, no change. I tried something rash after that and thought maybe it was an encoder issue and I swapped the encoder (hoping that with yaskawa absolute encoders they didn’t require careful phasing) well bricked that robot in the process as R is now totally out of phase , NP though as I only have one UP-165 controller this robot is now just a parts bot. I swapped that robot with the other UP-165. Robot worked great after I swapped the S axis servo (got a defective absolute data error) from the newly christened Parts robot. Robot worked well, a little creaky as it needs new grease (probably been out of service for 5-10 years), THEN I started getting the same axis R error as well as a alarm 1415 excessive segment safety. Does this sound like a problem with the robot or the R axis amplifier?