Otter, check out this thread when you get a chance: Batvan
Lots of ideas in there similar to what you and I have been talking about.
I particularly like his ambitions on RV'izing the factory HVAC system and his bed and storage box system. I've just skimmed it so far but it looks promising.
Here are some pictures of my floor deal. The 52 threaded holes are actually 7/16-20 nuts welded to 1/8" thick steel plates that bolt in at each seating row. Each plate reuses the factory seat mounting holes plus 3 or 4 newly drilled holes through the floor. Not swiss cheese at all.
This kills about 3/4" of my head space but I mulled over a lot of options and ended up settling on this one as a compromise between my "dream setup" and cost/time. One thing I'm considering as a permanent replacement for carpet is either 18 gauge sheet metal or 1/4" King Starboard. But like I said, I'm going to live with the carpet for now since I already have it.
The company that converted the van, CVC, didn't put a finish on the steel plates, so they rusted a little in the 2+ years of ride share service that the van saw. I knew that my use would probably expose them to a lot more water so I removed all the plates and sprayed them with cold galv. I'm reusing the foam spacers and carpet but I used lacquer thinner to remove all the carpet glue from the floor and plates -- I don't see the need for it and I want to be able to easily pick it up to inspect/clean.