Just came across your thread lakelover....nice ride!
I have a Jet as well and have really enjoyed the project...so far
I didn't have to replace my transom, so I can't speak to your immediate questions, but it does raise a question about how the motor will be placed and whether that will impact center of gravity/weight and how it performs. Is there a particular reason you want to have a higher transom? Just curious.
I know with mine it is a delicate balance and I have the cutout version of the transom. My boat pops up on plane quickly (1961 Johnson 40HP) and can be "slippery" in a straight line. I think these Jets have a very low profile compared to some of the others (Holiday, Jupiter, etc...).
Just something to consider. Good luck with your project.
If you're interested in selling your steering wheel let me know. I'm in the hunt for a vintage wheel

and not having much luck.
Wes