I did just this, successfully managed to edit everything with PK3DS, found the romfs directory with the repacker, repacked and then built as .cia, installed, and still absolutely no changes. My heart drops every time I run into the grass to find a damn wurmple.
Still,it's like the vanilla game.
Edit: Okay it seems I jumped the gun. After running into a wurmple on route 101, I lost most hope. But I continued anyway, to find an emboar level 2.
It must have been a really big coincidence to run into a wurmple first.. will test further.
It was an incredibly big PITA for me to go from never dumping a rom to a finished working(debateable, dexnav is buggy of course)version of OR .cia.
Due to this, I hope nobody else has to go through that. If anyone would be interested in a randomized OR .cia, just pm me.