So.... There were bumper guards on the rear corners and prow of the gunnels attached by bolts and rivets. Pulled the bolts and water gushed out. "This can't be good" So I cut into the bottom of the gunnels (I repaired the tops earlier but never hit the wood. The tops are a cap over an inner core) and this is what I found:

Major rot.

Ripped it out.

And cleaned it up (Not pictured, but I sanded out all the wood remnants and vacuumed it out). So worried, I also drilled a few holes into the transom to check for rot..... I didn't find any. The question now is to replace the rotten wood with new wood and a couple layers of glass, or pour in some 2 part foam, shape and glass?