Catching up on your posts. Your hull and stringer layout is basically the same as the 1990 Chaparral I just finished. I replaced the wood in the keel in my boat with CPVC pipe, peanut butter with chop as the glue, covered in 1708. Doinf this created a non-wood channel to direct water to the bilge between the bulkheads. I would imagine that the wood in the keel with glass over it was a structural feature. I did not like the idea of putting wood back since this low in the boat, it would be the first thing to rot.
That wood in the keel started all the way up in the bow where the bowhook goes through the bow, Again, not wanting to put wood back in this area, I used a block of UHMW polyethylene. This was glassed in with hairy PB, and numerous layers of 1708 for strength. The wood in my Chap's bow eye was completely rotted, and the eye could not be tightened any further.
Chines- All of the chines in these boats have a very thin wood strip in them. That wood strip will be holding water, especially near the transom. Do some exploratory cutting to find them. I had to use a vibrating tool with a metal cut-off blade to get mine out. They were a real PITA. My fear was that if I didn't get these strips out, the water could get to my new transom wood over time, or severely weaken the fiberglass. Again, I did not fill the chines with little wood strips. I simply used hairy PB, and covered the area with some 1708.
You can check out my restoration by clicking the link in my signature. I was there right where you are now, exactly one year ago.