First I would build a jig to cut the top like you said.

You would have to do the cross bar connections by hand and I would add rear port holes first so you can access the rear ones.
I would also first remove the Dagger board well with a dremel and a cut-off wheel.
If you are thinking about converting this into a F18 or lighter 18 you could change the dagger wells at this time as well. I would dremel along the top of the boat as apposed to a 45degree and also cut out the bottom also.
Good luck and take pics I wanna see it.
Thanks for the idea of cutting the deck from the hull from the top! I have a flat spot on a hull side to repair and had been wondering how to access the interior without destroying the existing hull / deck joint. I'm considering a triangular cross section glass / foam shelf bonded to the inside of the sheer of the hull to reattach the deck.