You're gonna have to start cutting on it sooner or later... I would wait and enjoy it before you deploy...
I don't have to many issues with my floor and dealing with water... Everybody down here is thinking about doing their doors the same way I did mine... None of theirs open or close any more...
And as far as welding the thin to thick stuff, blazinzuk is dead on... Run the bead on the thick and push it over to the thin... I did a lot to tack, tack, tack when putting my skins on... Then went back and welded between all the tacks...
Once you get after it, you'll have no problems... A little practice and you'll be a pro...
When you decide to jump in head first, start looking for a parts truck or pick up a bed and fenders to skin... It's a lot easier than working with the aluminum can skins you've created...