Take a look at the "transom time" thread in the Aquasport Rebuilds forum. Warthog5, for example, has posted an excellent tutorial regarding transom rebuilds. Spend some time looking over his pictures, links and commentary; it is well worth it. Also shoot over to the classicmako.com site and browse around.
Lay out your project on paper or your spreadsheet program and get estimates for epoxy, glass, transom core material and misc. supplies for out-of-pocket expenses. For a bill of materials maybe some of the guys who have done their transoms can provide a list.
One last thing: take lots of pictures. I'll need your experience & guidance when I get into my 33 year old transom...