I agree with ambush... I would also invest time in seeing where the leak came from, otherwise, you will be stripping the interior again soon!
I would use fiberglass as a cheap and easily available alternative to complete floorpan replacement. I bought a fiberglass repair kit from either Walmart or Home Depot (can't remember which) for under $20. You can get the regular kit, or (better for your application) the fiberglass gel kit. The gel kit contains some cloth, hardener, and a resin that has nearly the same consistency as Bondo. That should work great for your application, because you could simply smear that on without it all running through the pin holes. You can even use a foam pad or stout brush and paint it on the underside. I used the stuff for cowel repairs and it worked great becuase it didn't drip or run off.
Best of luck.