Fairly certain that PKHeX didn't fill your whole PC with bad eggs. Be sure that you didn't delete a byte while hex editing, shifting everything out of position.
The game has the "Player Appearance" in a non-obvious format and it wasn't really nailed down. It's a planned feature; those ComboBox dropdowns currently have no code associated with them.
For the next release I should have Pokedex corruption fixed (for the "Fill Dex" button), by copying in a complete version. Powersaves datamined one that was 718/721, but didn't have all the language/forms. With that I should also have all accessories and all regular items sorta like Powersaves does but smarter. Maybe for the clothes I can temporarily allow users to enter values into TextBox's instead of showing ComboBox's until we have a completely cataloged the association.
Release should be <24h from now, if things stay according to plan.