drew, nice pictures. Looks like it's going to be a great project. I started dealing with the immediate needs first, I purchased my boat after a fire so there was a lot of cleaning, about 80 cubic yards of trash and debris, next I cleaned, cleaned and cleaned some more. After I had a clean hull and cabin then I started working on all the systems that made it throught the fire. I got everthing working (two 6/71's and two 12kw gensets ((onan))) than I started painting the bilge. I am still painting the bilge. I would check your fuel tanks. You need good solid tanks if your going to build anything. Redue the fuel lines and vents. When you do make it to the topsides, I would build a subdeck over the existing deck and level everything out. That way you don't have to walk up and down a hill evertime your in the cabin. I attached a picture.
Look in the passage way and you will see the 2x4 that make the flat deck. These run above the regular deck to make everthing flat.