Ed, I'm doing the same thing on my transom. I was going to leave it open but have decided to flat across the back. I like the idea of added storage and or livewell.
As far as getting the wood out...... You are in virgin territory on that one considering it was not rotten. I know this sounds extreme but I would consider building a new transom skin. Many fiberglass guys don't even bother with wrecking out old transoms as it's usually more labor intensive unless you are trying to save the original gel coat. Considering you will likely paint the whole boat I would just cut it out and build a new one.
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[b]The Moose is Loose !
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