Layer Shift and Y axis Fails calibration  

Layer Shift and Y axis Fails calibration

Core One with MMU3 running firmware 6.5.3+12780  Slicer 2.9.4
This is the second attempt with similar results:
I was printing my first print using No Sparse Layers.  All seemed to be going well until it wasn't.  It was 80+% through before it had a color change and needed to wipe.  I was watching it (it's a 23 hour print) and there was a bad vibrating/grinding noise and it was shifted off worse than I was seeing on the print before that time.
I stopped the print and cleaned up and decided to make sure all was good before restarting the print.  This first time, it did the color changes perfect for about a cm and then there was a layer shift.  
I set the belt tension.  It was within the good zone for both, but I tweaked it to get it exactly on the frequency. 
I ran calibration and the Y axis failed.   I tried shutting off, making sure everything moved freely - no problem. 
Tried calibration repeatedly.   No solution.
Finally took things apart guessing that the motor was slipping.   I checked both X and Y motors and the grub screws were still tight.  
I reassembled the printer.  Ran calibration - same issue.
I went into the menu and moved the Y axis from one side to the other.   The full forward position was at -19 on the readout.   When I was trying to calibrate, it seemed to stop at where it would be approximately zero.
Anyway, after doing the full range movement, I reran calibrate Y (why not, right) and it magically was fixed!
I restarted the print.  This time when it got to the first filament change, it did a layer shift.  I reran the calibrate Y and it failed again.
I tried all the same things that worked last time and it does not work.

I plan to scrap the no spare layers and retry, but I cannot get it to pass Y calibration.  The belts are fine, the cabinet is square. 

I also tried doing a factory reset and chose only the Fix what is wrong (or whatever it is called) and that did nothing. 

Worth noting, it did pause in the print to tell me it was worried about a ceiling collision.  I have a MMU3 enclosed and there is plenty of room for movement and there is no concern about hitting anything.  I gave it the OK both times.  It was always after this point (by a few hours) when it had the shift, but it was something new.
What can I try? 

Thanks for any suggestions.