Sounds promising. Can I suggest one thing - take a breath and consolidate your understanding of the problem and that is truly is fixed (I'm about 90% confident from your description), before making too many changes.
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Need to understand a few other things too in UCCNC before I will be confident with it , but really only been using it over the weekend . I think I will prefer it to mach3.
One thing is when I change from Mach to UC (and Vice Versa) it "reinstalls the firmware for UC100 ?????
I set the pin numbers for the homing switches on each axis and now it will home , but I never really understand why I can jog through these switch positions . If I hit them in a program it will stop .
There is one helluva manual and It will take me some time to get to know the software . I will play for a day or two before I rehash the wiring.
Is there a reconfigure function in UCCNC I havent found it if there is .
I really don't understand this question - if you mean is there a profile system (so you can load different configurations) then absolutely - create/save profiles and load them from a modified icon which provides the machines name. Details in the manual - and I use this to run two different mills perfectly well (even with a cheeky M9998 to provide relay switching between the motor drives on the two mills).
If you mean can you configure pins/ports etc, I'm sure you're there already if you've got it working - hence my confusion. The only annoying thing for me is the constant Apply/Save mantra to not lose settings - but from memory Mach was a bit like that - at least on the motor tuning pages.
Just to report that changing the BoB to a PSU supply seems to have restored proper function so moving on:-
I have enabled soft limits and set what I thought were sensible ones but things dont seem quite intuitive particularly on Y axis but I think a new thread is callled for