Will the thinset I put down create a level surface and a good floor?

but I have now talked with 2 firms, and both quoted me a flat rate for each of the 3 above categories I listed - and that was with just quick surface level knowledge of my situation.

Not just spray Lysol, but wiping down all surfaces. 

Go big, and think of how you can invest in real estate in a highly scalable fashion.

My main advice would be to do your due diligence in verifying that your partner(s) and/or the sponsor is trustworthy & transparent, and that you feel confident in their contingencies, and also that they have a track record in getting their investors their money in a timely, professional fashion. 

Does the speed at which the orbital moves degrade the purpose of this step (pitting and grooving the surface for the paint to adhere to?

And besides cleaning, you have to disinfect every surface. 

Depending on the type of tree most feeder roots are fairly close to the surface, and given that there's a house on one side and a driveway on the other I would guess most of this tree's root system was in the dirt you just covered with pavers. 

I bleached every surface twice , yellow stuff just oozzing down the walls , the white ceiling fan was dark brown .

Just save yourself some cash and buy an investment property the old fashioned way.