Tue, all may not be lost. the standard transom on a 6.45 ribtec is too low and mine slopped water in. However I beleive yours is ex jet and therefore presumably has a flat planning pad under the stern. this means your 21" will start much higher and the top of the transom should end up with a half decent clearance from the water level.
Think what you need to do is glass back in the top of the transom by using a piece of formica to lay the gelcoat against followed by the GRP and marine ply. At some point it will need re-inforcing with transom supports to take 200 hp and you will probably want to do 2 sheets of s/s on both sides of the transom.