Z Stepper Motor Problems

I have a home built prusa I3v style printer. I had an extra SKR pro 1.2 and a tft35 for a CNC I'm not going to build anymore and decided to upgrade my old printer. Along with the board I upgraded to Marlin 2.1.2.1 and added some 2208 driver and a new extruder/hotend/cooling system. Everything went OK, I had some issues but got it to print fine. The hotend kept getting jammed and wasn't the upgrade I thought it would be so I printed some parts to make my new extruder and parts cooling work with my old hotend. I just got it assembled with the old hotend and set PID tuning and probe offsets in firmware and uploaded to the printer. I ran the z probe wizard and it completed fine and I noticed it was still using the old offsets so I reset EEPROM so I could run the z probe wizard with the correct offsets.

After resetting EEPROM now my z motors run rough and choppy. I've tried resetting all the feedrates and accel settings to default or lower and nothing seems to work.

If I manually adjust the z axis from touch mode they run rough and choppy. If I auto home from touch mode the z motors run rough and choppy x and y are fine. If I run auto home from marlin mode they run rough and choppy. However, if I manually move the z axis using the knob in marlin mode they run fine and smooth. I can plug the z motors into x and y and they turn fine, If I plug x and Y into the z headers they now run rough and choppy. It's obviously a setting or something I'm just overlooking. Any help would be appreciated.