Sounds like you have to use a rear transmission crossmember, and I'm assuming the side mounts for the engine.
I was concerned that you were setting out to use all the original stovebolt mounts and add a rear transmission mount which would be invitation for vibration and cracked housings. Engines and transmissions should only be mounted at 3 points (with a few exceptions).
You'll need to consider driveline angles.
tech tip
http://www.stovebolt.com/techtips/driveline/setup/index.htmlAnother Link to the manual (if temporarily broken in the tech tip)
http://media.spicerparts.com/media/details/kH7StMRqGZ9kzxSZMIf the new engine is at the same angle as your old relative to the frame then likely the angles will work out well, if not then you can adjust things to suit.
Seems you could use whichever mount fits the crossmember or transmission and adapt with new holes or an adapter block/plate on the opposite side.