I've replaced a few transoms. For me found it easiest to cut the inside fiberglass edge with a diamond wheel on a 4' grinder. Use a carbide blade on a skill saw to cut the inside transom into smaller manageable sections and remove them.
Usually the outside fiberglass skin is approximately 1/4', try not to damage that when taking the plywood layers out. Cut new plywood cores to fit, completely seal them with thinned out polyester resin. When dry apply two layers of fiberglass mat to the transom, saturate with resin, then apply one of the plywood cores.
Add two more layers of mat, saturate with resin, then add the last plywood core. Clamp, but use caution not over clamp. Might have to use some braces from floor,stringers or were ever you can to insure a good fit.
Sounds complicated, but its not that hard to do. Just a little messy, Oh when cutting and grinding be sure to wear natural fibers ...cotton, wool ect. cuts down on the itching.. definitely do not wear synthetic fibers.