there are really only 3 ways a stepper motor can skip steps.
1- it is commanded to move too quickly. (try the Mcode linked above to limit the max speed WAY slow).
2.- The belt or pulley slips. ( you seem to have that under control)
3.- There is something faulty in the electrical system (you are checking the wiring, but may need to check other electronics)
Done, it heads the right direction. Then hits the stops and keeps trying to go. Duh, I did not swap the stops. So I swapped the x & y stops on the board. It still tries heading into the stops. Awful noise. Put everything back and works fine with finding home and manual movement.
So I try again. swap & flip 180 the x & y motors on the board connections. Swap the x & y stop connectors on the board.
start in the middle of the table. Manually move the y 10mm on software, to move the x carrier. Horrid sound like it is skipping the pulley… but it is not. It is in the middle of the table and moving correct just the motor is making the noise internally. So I manually command a -10mm… the x carrier moves with the same noise, but in the +10 direction. After it stops, the motor makes a soft jittering noise. No movement, just the noise. I hit the main power switch after that.
I wanted to post an update with the problem resolved.
After reading on Reprap forums. One suggestion was to cool the board if the stepper chips are getting hot.
My stepper chips actually burnt my finger upon touch. Put a small fan on the board. I ave been printing great since the addition.
Thanks for the suggestions and help everyone.
Hope to contribute to this forum more.