No bites or community info, so one must roll-up-sleeves and put 2&2 together, Digging up a 328P pinout along with knowing ISP 6-pin assignments and my trusty DVM, I’ve validated all the ISP connections on the Carbide Motion ISP header and documented it for others who might be asking the same question.
Note that this is a v2.1 PCB picture, but suffice it to say this layout is consistent between rev’s 2.1 thru 2.3 (and I’ve read there’s a 2.4 PCB rev):
Next up, getting a bootloader that’s appropriate. The Arduino IDE allows you to burn a bootloader, however it doesn’t directly support the AVR JTAGICE MKII. There’s an AVR MKII choice in the Arduino IDE and I’ll attempt this bootloader burn.
I also downloaded AVR Studio which does support the JTAGICE MKII, but there’s no intrinsic “burn bootloader” option, hence I’ll try a hex file burn from AVR studio if the Arduino bootloader burn fails.