The IIGS Transwarp card doesn't have to be reverse-engineered. Gal Jedec files and Eprom binaries are available here:
Since the source code is also available, I'd replace t he GAL chips with a CPLD. Older versions of the Xilinx ISE tool still support the ABEL language, so it should be a very quick port. It'll save you the hassle of finding high-speed GAL chips, and it'll bring your design into this century by having JTAG programmability (note all the boards out there that suffered damage in a failed attempt of upgrading).
Make sure you keep that "mystery 40-pin connector" in your design, because that will be the place where you can add a 65816-replacement board (hint: Bill Mensch is not easy to deal with, so I totally understand and support the decision of keeping a backdoor open).
I was approached multiple times because people wanted me to build such a thing, but I never got around to doing any reasonable kind of research. However, Apple-retro is currently hot: There has been an auction in Bochum, Germany just a few days ago where an Apple 1 has been sold for 400.000,- EUR.