I had two issues:
- The manual says that you must add a shim to the motor pulley, If I use the shim, both motor and spindle pulleys were out of alignment. I ended not using the shim in order to have proper pulley alignment between motor and spindle.
2.- For the encoder installation procedure, the threads on the head column were completely off for alignment , for attaching the encoder to the head base. I had to make a slots to the encoder using a dremel.
3.- Every time I went to running the encoder test, was failed. At first i thought I had a bad encoder, I even bought another one, but i discovered that I had to run the spindle first, let say 1000 RPM BEFORE doing the test or it will failed because it said that the alignment was bad , check for alignment and try again.
After running the spindle before the encoder test, the test pass good. I never had a problem with the ATC also.
Good luck with the upgrade and check for these issues i had.