I found some fixes to the issues with this hack (which, by the way, I am thoroughly enjoying), so here's a modified version of the challenge mode. I changed the type effectiveness chart so that dark is immune to psychic, dragons are not resistant to ghost, and one other thing that eludes me at the moment (but I think also involved the dragon type).
I also used the patch by DoesntKnowHowToPlay which seems to have fixed the physical/special split.
Oh, and I couldn't find Lapras on route 124, so I have them appear in the wild there. Did I just miss that event?
Anyway, here's the changed UPS. Let me know if it works!
www DOT dropbox DOT com/sh/iehimtx0hmhda73/AABHbbraueSyFjfUcM-holU4a?dl=0
P.S: I guess I can't post links yet, so sorry about the workaround.