I just did my KM3V on a 3GM30F. To align the engine to the shaft adjust the engine mounting bolts so that the KM3V flange and the prop shaft flange are parallel within 0.004 in or so measured at the outer edge before pulling it tight. Same as regular drive with a little mental twisting due to the backwards mounting of the engine.
In my boat (Vancouver 36) the shaft comes out the back (of the drive) toward the front (of the boat) thru a opening. It won't come out the back (of the boat) with the rudder installed. The old prop flange wouldn't come off so it had to be cut and replaced. Bad scene. Good opportunity to replace the cutlass.
I think my engine is reversed mounted. There is a hole in the transmission that the prop shaft comes through. Then it looks like that is whre the coulpling is. could your prop shaft go either direction on the transmission?