I have used paper templates numerous times. They work just fine. The only thing the jig does the paper doesn't is it holds the drill at the correct angle.. You can do this your self if you pay attention and/or a friend assists. Lay out the transom before you make your final call as to how much needs to be filled..The holes will not only be moving out they will also be moving up. Make no assumptions as to where the holes will be .. Verify by laying it out in advance! The work is in the process. whether you add 4 inches or 8 doesn't change much.. Yes, I agree if the entire transom is sound just modify as needed. Never heard of soaking the wood. I would not suggest that. Use at least a 3" overlap. I think I would lean strongly toward removing the false floor and adding the center stringer. Either way take a good look at the outside stringers to ensure they are in good shape.

I think 1 1/2" minimum clearance between the engines would be good.. The turbo housings will not like bumping into each other under way