Hey Jeff --
This should work just fine.
You definately want to close up the holes in the firewall and while you're doing that you can knock out the blind nuts and plug those holes too. I generally just insert a piece of the appropriate sized dowel as a light force fit into the hole and then hit it w/ CA and sand it flush. Then you can mount the engine however you want. Throttle linkage/servo location can be worked out after that. And while you're in there I'd suggest that you reinforce the gear mounting blocks. Scabbing each side w/ a piece of ply'll do it.
Good luck. It's a great flying airplane and that OS 46 will make it honk.
Al