Every time I've had that situation I've thrown away the pre-hung casing and built my own, so you're one step ahead already. The bottom line is -- you've got to construct a casing that will:
1) provide a plumb face on which to mount the hinges
2) allow the door to swing free without hitting the floor or ceiling
3) fit to the door when closed
4) fit to the house.
This can all be done with the pre-hung casing, but I've found it easier to roll my own. I spend a lot of time on Step 1, and the rest fall into place pretty easily unless you've got a really nasty situation. A good carpenter can hang a pre-hung door in under an hour; I spend 3 or 4 hours on Step 1 .
Full disclosure: I am not a plumber, nor am I a carpenter, but my pipes don't leak and my doors swing free (mostly).