Successful stepconf user buys Mesa5i25 wants to use experience in pncconf. How??

For example, the XML file for PNCConf says StepGen instances = 10, Encoder instances = 2.

That's correct
There are 5 stepgens per connector (4 axis and 1 for chargepump per connector)
the are encoders available on G540 inputs if desired but these in no way interfere
with the normal use of those inputs

But I would say my biggest issue is not understand how PNCConf will "connect" my choices to the hardware's pins.

I have XYZABC. Previously, I had XYZA and used an LPT port (with pull-ups) and assigned the pins in StepConf.

I fully understand the Mesa board is far more powerful and flexible and I look forward to using these features in the future. But I had thought that the presence of a "G540x2" configuration would be as simple as that sounds.

I can't manage to equate the "Num" column with anything.

What's the difference between 000 and 0, or 001 and 1 ? What is "Num" indicating?

The pin assignment of thing like stepgens is not changeable,
it is determined by the specific firmware loaded in the FPGA.

So a G540 configuration assigns stepgen pins in a Gecko G540
compatible manner:

Stepgen 0 = Gecko G540 X
Stepgen 1 = Gecko G540 Y
Stepgen 2 = Gecko G540 Z
Stepgen 3 = Gecko G540 A

etc

OK.

PNCConf prompted me to complete scale information on XYZ and A. But only once -- for one G540, I guess.

Do you know what file(s) I'll now need to edit to enable the other G540. Is it just the HAL file?

BTW, what does "Num" indicate on PNCConf? What is the difference between one of them being number 000 and another being numbered 0 (likewise, 001 and 1) ?