You are allowed to use MS Paint. "External tools" means things like the Witness Trainer or Autohotkey.

External tools also include things like puzzle solvers - generally, as long as you're doing the solving yourself, the inputs yourself, and not modifying the game beyond the randomizer, it's fair game to use.

So for instance if you wanted to keep a set of physical shapes near you to assist with shape puzzles, that's legal.

Also, AutoHotKey is specifically disallowed for macro/automation purposes. If you use it for a key rebind (one to one) then that would also be okay.