My opinion does not come from experience, so take it for what it's worth. My boat may never get redone, the PO put a new floor over the old one, and from an operational standpoint, it's fine. The only stringers I worry about are the ones under the motor. I'd love to dig in to it and do a nice rebuild, but the boat lives at my cottage, and I want it in the water all summer, so I'd need heated work space larger than the boat in order to re do it.

I strongly believe that if you don't have the original mold, taking the cap off greatly complicates the rebuild if you want to get the hull straight. A great amount of the strength of the main structure of the hull, is the box that is created by the floor being bonded to the hull at the sides, and then tied together by the stringers. The remainder is provided by the cap being tied to the hull. Pulling the cap and the floor leaves you with a flexible hull. If you replace all the stringers and bond the floor back with the hull flexed, it'll stay that way. At least if you leave the cap in place, when you remove all the structure of the floor, you'll still have a shot at keeping the hull a bit truer than had you pulled the whole thing apart because the cap will somewhat hold the hull true.

Don't get me wrong, I'm not saying it's a bad idea to take the cap off, just that there are some advantages and disadvantages to doing the resto either way.