BTO, I just replaced my transom and floor on my Omega last winter. I also changed stringer config to full length from the orginal "goal post" setup. If you have any ?s feel free to shoot me an e-mail.
Also, you might as well plan on flipping the hull and taking any hook or rocker out after the work inside the boat is complete.
After making all these changes, my Omega is a quick and smooth ride.
Good Luck!