To answer your question about UCCNC - as a replacement for Mach3 it also requires that you replace your breakout board with a UCxxx/AXBB motion controller. Beyond that, your stepper/drivers are okay. You can read the requirements for UCCNC in terms of host computer for yourself.

Regarding the behaviour of the input limits/estops - you mention bugs, faults or stupidity - the latter is the only one you can fix at low cost :-). Disable your limits within Mach3 and get the estop working predictably. NC/gnd is the better solution - you provide a direct signal path in this case (ignoring that this solution is safer for determination of circuit failure) - I don't know your BoB but some/many require two separate supplies - 5V and a 12-24V - the latter regulated onboard to use as the drive supply for onboard opto-isolator inputs - without that your inputs may not work (but generally just "don't work" rather than be sporadic). Some other hateful BoBs I've encountered don't isolate the inputs and just present the parallel interface of the computer straight to the BoB Input pins (maybe a pull-up and noise suppression cap) - these are highly susceptible to noise and can cause spurious triggers. Mach3 has some debounce settings to attempt to filter electrical noise. A photo of your BoB would help.