You should not need to run the engine with the alternator disconnected. Having said that you an just pull the field wires as well
If the drain is alternator connected, simply disconnecting the output wire with engine stopped should show up as reduced battery drain.
Is there any aftermarket equipment in the car?
How about trunk lamp? Have you checked the glove box lamp?
How about the "key in" / delay stuff? I don't remember how all that is wired, I'd have to look