The S-100 V2 board uses an Atmel AT1508 CPLD, which can be programmed with the ATDH1150USB “cable” from Kanda
Unfortunately John uses a different programmer from Rockford, and has a 6 pin connector instead of the more standard JTAG-A.
I made up a small adapter to simplify the connection.
I included a small LED (use a 1K resistor) to indicate when the board is receiving power from the 80386 board.
I couldn't locate a 2×3 pin IDC connector, so used a 2×5 pin connector. I use pins 5-10 and just let pins 1-4 dangle over the edge. This way it doesn't bump into the card ejector.
Just be careful making sure you have pin 1 oriented correctly.
I'd suggest you plug the adapter into the S-100 board first and make sure the LED lights up.
The files are shared at OSHPARK: https://www.oshpark.com/shared_projects/DlGbC4Hr
Or you can download the Gerber files here: jtag.zip
Cost is $5.55 for 3 bare pc boards fabricated and shipped.