Must be a bulkhead - looks like it's separating two tank.
Kyle, I feel for 'ya. That must be like a kick in the gut.
If you're comfortable with the repair - go for it - just realize it's going take a lot of time and the amount you need to repair will get 2 or 3 times larger than what you think. Sometimes, it's more about knowing when to stop otherwise you end up just keep going and going and going with the destruction phase.
For the kneewall, you could cut the top off like you did and than also one side. Don't cut flush with the floor or transom - leave 1/2" or 1" "lip". You can even re-use the cutoff sections of glass along with a layer of something like 1708. You'd overlap the 1708 on the floor and over the top of the kneewall. The bulkhead can be cut out and tabbed with glass into the stringers. Obviously the tanks need to come out... which is probably good to check and consider replacing as they sometimes get holes in them from lack of air circulation around them. And... you might as well replace all the fuel hoses, as well. See what I mean? It can be like going down a rabbit hole.
Depending on how much you paid and what you what to invest (time and money), you may consider parting it out. Don't get me wrong - it's all fixable - but you really need to think things through before you too far into. Enlisting the help of a pro to further check things out may not be a bad idea. But since you dove right into drilling the kneewall, you may very well be capable to figuring it all yourself.