Aluminium Profile Type Router - Initial questions

[CNCRY]

Will post some progress photos soon, but have now pretty much completed the wiring and physical build.
Cable chain finally arrived from China so the (crazy) amount of wiring is now running back into the control box and 4 separate limits wired in.
I setup the limit and tested jogging into them and all good there. Machine is running at 4m/min currently as Jazz suggested, until I tune it further.
I ended up straightening the ballscrew mostly, using the advanced method of compressing between some hardwood and rotating it. But now it's back in the mount it seems to be running pretty well at 100% jog speed. I think my drill test made it seem a lot worse plus there was some slight misalignment of the motor coupler. I do notice the X axis is very smooth even compared to the dual Y.
My next test after jogging was homing.

So X and Z - moved along, hit the limit stopped and backed off - great.
Dual Y - both axis moved towards limit, one side hit limit switch fractionally before the other, then the one which hit the limit seems to keep going and the other side never hits the limit, so the gantry starts to go off square and hit the ESTOP before it breaks the gantry!

I have both axis set to have homing to the negative limit and 2 separate limit pins set so not sure what is going on here.
When I jog the axis slowly into limit it hit both pins and stopped, both flag up in UCCNC as hit.

Before I post on UCCNC forum am I missing something obvious here in the homing sequence for dual axis?