The way I look at things is that all capital allocators are spread traders underneath it all, maybe real estate more so because of our common sources of funds. 

It will say your business name and underneath "Client Trust Account."

If it were mine I would replace the roof, including any roof decking underneath the shingles that need to be replaced, and look into the cost of doing a ridge vent at the top.As far as the air conditioning system , you might be replacing a well built heavy duty unit with something that has a much shorter service life and instead of using freon it uses some incredibly expensive chemical . 

The last tenant had a suction cup mat down and whatever cleaner they used just sat underneath and ate the finish up.

You will have to pay for surveys, plans, possibly a soil sample (elevation certificate if in flood). 3) Build- Once plans are approved and your financing is lined up, you can start to build. 4) Certificate of Occupancy- Complete the build and all inspections and sell.

My gardener went to remove a tree that was growing roots underneath the foundation, and when he sent me photos, there was cigarette butts all around the back patio and front of the house

Some things that might be a concern:1) Obviously have to make sure things are all permitted first2) I don't want the room to "feel" like an addition, so flooring has to be same level/standardized with the rest of the house3) Unlike the rest of the house that has an identically-shaped 2200sqft basement underneath, this added space will not have a basement directly underneath it -- I'm not sure if this poses major cons for some reason that I'm not aware of4) Especially given the lack of basement underneath, I have to make sure that the HVAC can still somehow be piped into this room#2 and #3 are probably my biggest concerns (#1 and #4 I can find out relatively easily)Any tips/thoughts or other experience would be greatly appreciated. 

Step on is decontaminating the site, probably busting out the concrete floors and if necessary the soil under it.

However, I don't know if there's been soil tests, building plans, I don't know if there's utilities in place underground, if it's in an HOA, etc.. 

I have a holding company LLC as well and a few other LLC's underneath as operating companies with the holding co being the "sole member" of the operating LLC's as you've described.