Y axis stalling

[JAZZCNC]

Thanks for the help. How can I tell if the alignment is off to bend the leadscrew? And is that fixable?

With careful measurements and visual checks.!! Aligning ballscrew and nut is tedious job but very important to both prevent bending and getting the best performance.
If alignment is off enough to bend the screw it should easily be visible by manually running the gantry along it's length carefully watching the screw to see if it's bending. Also if you turn the screw by hand with motor disconnected and you feel it stiffen has it nears ends this is good indication some things off.!!

Can't really comment on what would be needed to fix without seeing how ends are fixed and how much off it is.?