I ended up doing exactly what you suggested - I spent a couple of hours this afternoon looking at board to board connectors at Digikey and Mouser and couldn't find a match, so it was on to plan B:
I spent at least a couple of hours under the microscope scraping each individual pin in the 2 connectors on the bottom side of one card with a sewing pin, and a very fine tipped "grinding pen" (if you watch Northridge Fix on youtube, you know what I'm talking about) bit just by hand. I also finished up by running a spatula with printer paper wrapped around it as a final "polish" back and forth in the central slot of the connector. That's a trick I learned many years ago - printer paper is just abrasive enough to use for cleaning up contacts without damaging any of the metal of the connector. Also used the pin and some cotton from a cotton bud and acetone to soak up all the mess, and some compressed air to blow out what was left.
First time I ran the cards together, I had 2 failing self tests, inter-chip resource bus and one of the clocking tests both failing on the slave board. Took it apart again and did a little more scraping, polishing with the printer paper on the spatula, and cleaning again with compressed air, and on the second try, it's working!
I did also use a tiny dremel sized brass brush too - again, by hand, not in any tool that would spin it, and I tried cleaning the contacts on the bottom connectors of the other board without doing any scraping first - it definitely didn't get some of the bigger "chunky" stuff off, but it looks quite a bit better. Scraping each pin individually is definitely the way to go. If I get some more boards in the future and need to use the bottom connectors on that board, I'll have to do some more manual scrapey-scrapey under the microscope to get those contacts in good shape.
All in all, the plating doesn't look perfect anymore, but it is working.
What an absolute journey it's been to get to this!
2 Cards linked together into one "analyzer", the IA compiled and inserted, and actually seeing all of the defined buses now! And 2 sets of the cables I bought showed up today too, so I'm technically ready to run this! Now I need to get the target system ready - that's a bit of a project in and of itself. Tomorrow - I'm way too tired today.