As for debugging, why not just put checkboxes in the input-output lookup table(s) shown on the left. And highlight the currently input line + mark wrong outputs. I think that would be intuitive.

To further build on this; If there is an intermediate state, show its pins in the diagram like output and input. If the table becomes wide, perhaps show it on the bottom. Perhaps let users add a "debug probe" from the toolbox that becomes a column in that table.