Alright we figured this out.

So here is the procedure if this don’t work for you I’ve listed everything we did and what results it yielded.

Encoder change = no improvement
Encoder cable change = no improvement
Changed Endat card = no improvement
Swapped A & A- channels = no improvement
Swapped motor leads = no improvement

This is what worked

Put tension on rotor using chainfall and strap, performed AutoAlign U10 also changed A1 interia to 1.00 from 2.00 (read in the book this would make the shakes less violent) = no more violent shake

Now we tried running and got Encoder Fault (ENCODER FLT) we swapped 2 motor leads = Good! Finally moving no faults in opposite direction.

Changed direction on C1 Motor Rotation: success!

Conclusion when performing auto align and nothing is working out tension(LOAD) on the sheave do an auto align not Open Loop.