So I ended up pulling the cards (except for the CP-A), testing voltages, and adding just the MPU and 1st RAM card back, testing, then re-adding the remaining cards one at a time - each time reentering the small test program from the assembly guide. After the cards were all added back I entered and ran a few other programs I found on on the net, including the "cylon effect" program for the programmed output lights I found on Lawrence Woodman's site.
To net things out, the system seems to be working (at least the CPU and RAM -- haven't tried to do anything with the IO boards other than verify the system continues to behave with them in place).
I am having an issue though, with the deposit next switch not working -- but only on one of the RAM cards.
For some reason, deposit next is unreliable with the first memory card. It will always advance the address, but will usually not write to memory (it seems to always store if all 0s, but but for nonzero bit patterns it will usually store only a subset of the 1's). The deposit ("up position") switch always works, and I can enter programs by using deposit next to advance the address, then flipping the switch up to actually store. At first I thought there was an issue with the switch itself, or with the circuitry on the CPA, except that deposit next works flawlessly on the other 4 memory boards.
The problematic card is an MITS 16K at address 0000. The other cards consist of a CCS 16K, a couple of Music 4K cards, and an IMSAI RAM4A. All are static memory cards. I can deposit/deposit next and examine/examine next memory on the other cards without issue (some of them even have LEDs that light up when the memory on the card is accessed).
There's not much in the way of configuration on the MITS card -- just a single dip switch bank used to set the base address.