Continuing my reverse engineering efforts on my CMS 9619 and 9609 SBCs, I downloaded the ROMs that were still in two of the boards. I inserted the ROMS into an Apple IIe's Super Serial Card ROM socket, and transferred the data using the IIe monitor. I used a similar technique previously to program EEPROMs on the Apple IIe.
With the ROM data in hand, I began machine code disassembly. Unfortunately I don't know 6809 assembly code, but with the help of the source code from an earlier version that I found online, I was able to figure out a lot of it. I started a new CMS_ROMs GitHub project to keep the code in. It includes a makefile that translates the original Apple IIe monitor dumps into a hex dump, then a binary, then disassembles it.
Also, DaveW was kind enough to scan and post his documents for a CMS 9639 SBC that he has. It is more advanced than the 9609 and 9619 that I have, and includes an MMU. Great information there that I will need to spend some time looking at.