As far as I can see, the best course of action would be to extract all those Pokémon to .pk2 files. Afterwards, create a new Pokémon Crystal save, edit it in PKHeX so that your name and ID match, insert all those Pokémon with PKHeX, then play through the game again to have a finished save. Or just download a finished save and edit the info to match yours. Both would work. I'll play around with your file anyway and see if I can get it to run.
EDIT: I managed to make it run and save in mGBA. You still have a lot of corrupted Pokémon, and the save file won't open in PKHeX so that we can batch export/import Pokémon (and PikaSav's .pkm files won't load in PKHeX), but at least it's playable. If I find any other solution, I'll let you know.
Crystal.sav