my Lyman project continues

Well I got her off the trailor and into a sling and started stripping the years of paint away. I was surprised to find there was bondo in my transom! It was used to fill in rot from where the iron bolts rotted away the wood which runs almost all the way across about 1 inch thick and thru the mohogony outer wood and the inner ply wood. I was thinking of just using a router and guide to cut away the rot using a small router bit with 2.25 inch height and just router out the rot and then just machine sone new mahogony planks and then glue together. Anyone got any other idea's??? I also thought about using a bevel cut and then reverse beveling the fill piece but that would take a huge chunk of good wood out and I don't want to do that. I have the mahogony and ply but don't want to jump right in.