Nate,
I know on my Klein sprinter the bottom of the flywheel is slightly above the bottom of the chassis plate - it needs to be that way so you don't kill the engine when the chassis bottoms out on the dirt on bumps. I don't need to run any spacers on my engine mounts to make the clutch bell clear the chassis - maybe it's a difference in your motor/clutch combo? You may need to grind out the chassis opening a little to achieve the clearence. In regards to engaging the starter wheel and flywheel...this can be a ricky setting. the starter wheel needs to be exactly in the center of the flywheel opening to allow it to enter the opening as far as possible. If the starter wheel is worn (smaller in diameter) it can be an issue. I have been known to shave the starter wheel mounts to set the starter wheel up a little higher to compoensate for wear. Starter boxes can be a real hassle sometimes!!
Hope this helps....
Jerry