Same problem here :/
the only solution i get is take a .sav created by my R4 from the (U) version, then pokesav it adding the pokemons i got on the japanese, changing OT, ID and stuff to make them obbey, and getting a 'Walk trough everything' AR to make it easier to get where i was. It's a matter of a couple of hours.
the only problem is that the AR code isn't available yet and when finished you'll have the whole johto trainer set unbeaten.