Homebuilt boats tend to be heavy. My experience is that pontoons don't carry weight all that well, and they will draw MORE water than a similar sized flat bottomed barge hull. If I were to do as you propose I'd get a good ALUMINUM barge hull and go from there. Old fiberglass hulls are usually reinforced with wood, and have rot issues. Even though I love my diesel, for a boat that isn't expected to move a whole lot I'd stick with outboard power. I/O would be my LAST choice, after paddles. My next houseboat probably won't have an engine, it'll have a remote controlled push-boat that will double as a launch.
I'd get the widest hull I could find, and build out to the edge for maximum space in a given length. If you REALLY think you need walkways, add catwalks (I've never found the need).
Keep everything on one level if possible, split-levels are a PIA.
Just my opinion.