Which Do I Use: PnCConf or the Config tool from GitHub

You check whether the pinout matches your hardware by looking at the .pin file.
This is independent of pncconf. Are you saying a G540 configuration matches your hardware pinout?

Yes, the pinout of my controller matches the G540 pin file.

I appreciate your help, but it really seems that this product needs a LOT more work in terms of documentation and software implementation.

I have to say I am REALLY disappointed with this purchase. This is not a very complete, finished product. It is really a testament to how un-finished this is when It has taken HOURS of my time combing through forums and web pages and docs and youtube and other stuff, and I STILL cannot get enough information to output 3 simple step and 3 simple dir signals out one port. I don't event have e-stop, limits, or a spindle!

I am really sad about this because I have used LinuxCNC for years using the parallel port without issue and due to PC failure needed an alternative.

I have just requested instructions on how to return this for my money back.

If you cannot get motion on all three axis, its most likely
that the loaded firmware pinout does not match your hardware
or that the step times are too short for your hardware.

This has been solved and the recap is here.
forum.linuxcnc.org/27-driver-boards/4294...2-and-tb6560-drivers

JT