Hi, Spiwrx
Sounds good, If Your Happy with the Speed, Lot's of figure's get bounced around on Stepper's
On the Y limit, Maybe a bad SW/Contacts, Some have put small .01 disk capacitors across the SW terminals, pull up or Pull down resistor's, Re-check the wiring, Swap the Switch's
around, or Let it work for a while,.
Are your SW's N.C. in Series or N.O. in Parr.
If you have a O-Scope you should be able to track it down at some Point.
Have Some Fun Sounds Better, Chip