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I'm sorry to bump this, but i just read through this thread and it's obvious that the problem is the JAPANESE pokemon breeding with the NA pokemon, not 3rd/4th gen.
"Though I have never tried to cross gen breed with two US game Pokemon."
um... yea you might want to do that XD
To my understanding, it will gain the stats for all of the EPs you fought, but of course it will keep them consistant with your level. You won't magically get 100 lvl stats when you're at 91. But with getting max EPs at level 90, you will level up and have max stats for a lvl 91 EP trained ampharos.
1). I'll be transferring my tyranitar from emerald over today (adamant perfect attack DV, lv100 :D . Can't remember exact EPs, but i know Attack is maxed and there is some in HP)
It knows Rock Slide, EQ, DD and Crunch. If i want to use it for the BT in DP, is this its best moveset? If not...