Y Axis offset itself while running

The important thing is, you found the issue.
Nice!

Good job troubleshooting!

Still highly recommend getting the tuning cable and software.  There aren't a ton of settings which are understandable, but the alarm output polarity, following error, and micro-steps are all pretty easily handled in the otherwise horrible software.

If you do a search from a few months ago I posted some screenshots and descriptions of how to navigate the stepperonline Y-series tuning software.