Funny you should mention that, I was about to point it out but I see you are thinking clearly and correctly One change leads to another. Here ya go...One more request. Can I see a pic of the inside of the rear transom? I am curious how much clamping board that you have left.
I have 5 " of clamping board left, that's plenty, but your idea of cutting the transom down first, then making the clamping board makes sense, especially since you are lowering the sheer. That's probably a better approach than mine. My projects tend to evolve, rather than be engineered from the start, but the end usually hides the means
As you surmised, the rear seat is almost 15" high. With a 15" transom we will either have to lower the seat, or make a cut out in the rear seat top to provide clearance for the motor clamps. Not sure yet just how I'll handle that, I don't think good when my brain gets over 100 degrees.
Think I'm going to give it a rest and head for Lowes, pick up some yellow pine for battens and a couple dozen disposable brushes.
Keep on thinkin' AH, keep us out of trouble