Thanks for playing, I'll add the notes to my ever growing collection of stuff to fix.
I got really worried about the puzzle actually but I ended up doing the same that I did for stage 8 which is to make the penalty not that big a deal. I also don't have too much confidence in the bugs because they are real time elements in a turn based game and that rubs me the wrong way. Then again, pausing them would make them even less threatening. Perhaps more bugs are required? Who knows.
As for the clue, here's another one:
Also, balance is really hard. Now I understand why in most RPGs the beginning and end are the hardest parts.