Wah, I'm so sorry you went through all that trouble! The bad end was made so that it was the hardest to get unless you wee blatantly mean.
But I checked out the issue, and it's true there was a sliiighht little hitch in the coding side and all this happened because I typed the walkthrough from memory.
Anyways, will be uploading the fix soon.
For now, Quickfix, I've edited the walkthrough... T^T . (If you still have save files from your previous playthough, just choose one wrong option ie 3/4, so maybe Accuse the pink girl at the aquarium and it should lead you on Atsu's path)
(I wanted the good ending to be available even if one mistake was made, it ended up being that it would only show up IF that one mistake was made)
Again, really really REALLY sorry for all the trouble! I hope Atsu'll make up for it! T^T