I know this can be considered completely unrelated, but I've asked this before.
Is there any reason in particular you haven't decided to rebuild the game from scratch in a different engine?
I feel like if you did this in unity or game maker You'd have access to much more tools and assets, and getting to the state the game is already in would take not time at all.
In my honest opinion it would even be easier to make youre own engine than to decrypt and reverse engineer what gamefreak did.
That or Just use Jpan's hacked engine which is 1000X more flexible than what you seem to be doing.
All though even after searching for about 30 or so mins i could not fin a download for it.
that might just be me though.
Edit: I legit just found the Hacked engine download after typing this Rip. im gonna try to get into that and make some edits to what i have to see if i can help resolve the weighting issue.
Edit2 : i think my lack of knowledge as far as roms go i really showing here