Gimme some time. I got the save file on my computer from the cartridge but I'm having power outages from bad storms. I've not used PKHeX but I assume this may mean I need to alter the save file to function on the DS Virtual Console in some way? All I did was try to use the file converter to change it to a sav.dat file.
Alright, sorry for the wait. I can open my save file in PKHex and see all my Pokémon etc. I have an error that says, "Unable to match origin of a Pokémon" Which may be because some of these Pokémon came from Pokémon stadium's storage box from prior games(?) Is this what is holding back my save from working on Virtual Console??
EDIT: Ha I see the Pokémon that is flagged is an Aerodactyl from stadium that knows a move it shouldn't haha. If I take that out will it work???
I forgot to hit the quote button in my reply...