You can interrogate the hardware interactively for those really thorny problems and confirm your hypotheses immediately. You can write short test scripts and send them via the terminal and/or write and send short Assembler routines and test those interactively. Each routine you define is interactively usable to assist with higher level testing and/or can be further compiled together to make higher level or looping tests.
It's old and it's weird but it's still a good tool for this kind of work. It may mean you only have to enter the top domain of Hell. :-)
https://mecrisp-stellaris-folkdoc.sourceforge.io/flashing-me...
*I have no connection to mecrisp Forth but know it to have a good reputation. It is a a native code compiler with an integrated text interpreter.