Thanks for pointing out those gotcha's!
The subtraction thing is a clever implementation trick, I think I will try that in the core. The ALU already needs to support "A and not B" for instructions like COC and SZC, so must have complemented B available anyway. Doing subtract as "A + not B + 1", where the "+ 1" is done by setting 'carry in' to one, means that the ALU only needs to implement an adder and not a subtractor as well.
The MDEX operating system ("CP/M for the Marinchip M9900") has a program "BRAINS" that does a memory and a CPU check. However, I only have the executable, not the source. I'm not sure how thorough it is, it may only check for some common failure cases (e.g. CRU drivers fried).