pdnt.axis.jog-counts is connected to the raw pulse coming of the driver pin if you’re not getting any activity at that pin then I would think you have loaded the wrong driver or the hal program / the ini file is missing something. If you look at the 2.8 docs it shows 3 drivers for similar pendant (xhc-hb04-accels, xhc-hb04, xhc-whb04b-6) the developer of the 3rd driver is indicating that his driver was only tested with the 18 keys pendant and he is not sure about the 16 keys. I think your pendant looks similar to the xhc-whb04b-6, so make sure that you are loading the proper driver.
Question about your milling machine, does it have ball screws? if not, are you planning to install ballscrews? I have similar machine (Bridgeport clone) I was looking at ground ball screw on eBay, but the cost is more than I paid for the machine. So, I am looking at Chinese rolled ballscrews, but I am not sure how good they are. Do you have solution for the Z axis motor mount …?