wow!!!
Huge job pal but totally do-able
Things to consider are which has the best hull to start with. Do you have a moisture meter? Check the hull, stringers and gell with the meter and see if they are dry or saturated with water. Obviously the dry one is the one to build.
I am not sure from your post why you want to separate the top from the bottom but It is a big job and you need an overhead crane or at least chainfalls and some swing sets or something.
As for the fuel systems there are access hole for inspection and the tank is aluminum and should pose no problems? If you smell fuel, it may just be a dried or cracked hose, and this means you don't need to tear up the floor, just change the lines!
Some things to look for are wet rot on the engine mounts and lower stringers. The main cross stringer behind the seat is always a good place to check. If your vaccuuming out wood chips then its time to replace the whole thing!
Evaluate the job carefully and see what the boat really needs as what your describing is a big job. I am helping my friend do a set of stringers in his boat right now and let me tell you it's no picnic! It will be nice when we are done as he spared no expense for good wood and proper materials.
Hope that helps?