> It still produces a lot of crap in the later steps (understanding the implementation itself)

I've had success here by adding a phase called "grounding" that attempts to verify its "understanding" by creating tests that modify the running executable to ensure its made the right inference.

Is this variable really MARIO_X? Change it and see if Mario moves. Etc.

As an example in Donkey Kong - the system had trouble deciding if an array controlled barrels or fireballs. There was conflicting evidence.

After many trips through the loop - it realized it does BOTH, depending on which level you're on.

So the "understanding" grows with each iteration.