EdwinRR

Sounds like the dumper is adding extra data around the actual save. I'd try trimming the save to the raw 32 KB, edit it in PKHeX, then pad/rebuild it back to the original 128 KB format. Someone with the same GB Transferer II should know the exact layout.

You could check the pret and pret-disassembly communities, they've documented a lot of the Gen 1–3 internals. If it's been reverse-engineered, that's probably the best place to start.

If dumping the save turns out to be too much hassle, I'd probably go the GameShark route and read the stats directly. Hopefully someone here knows a compatible dumper for Stadium's FlashRAM saves.

A Pokémon MMO with all regions would be amazing. Co-op story is probably my biggest wish though. I'm not totally sold on replacing turn-based battles with full action combat, but having it as an optional mode could be the best of both worlds.