To remedy that, the carpets should be ripped up and sealant applied to the subfloor, at minimum.There are also tiles in the smaller upstairs bathroom that are lifting up and creating a safety hazard; putting a rug on top is not a sufficient solution.The house is in a condition that materially interferes with the health of household members.

PM says that whole house requires repainting on the interior including cielings and that "sealants" might need to be used for cracks in certain areas.

You could do a roll on silicone roof sealant. 

3) Aside from washing the walls or getting a full repaint quoted, would it be reasonable to deduct the expected cost of "Kilz" paint/odor sealant brand for effected square footage?

Often there is not enough sealant around the bolts that are put in and not having proper drain lines to lead away from the roof itself leads to ponding.

If you seal the concrete, then whatever's in it, including odor, will be trapped under the sealant.

Just not as long as the EverSeal System.We have installed the EverSeal system on many Rubber roofs without any issues in conducting repairs to the rubber before or after the installation.The sealant is built to adhere to rubber extremely well and we have techniques that allow us to make repairs to these roofs before and after.

I can see that someone has tried repeatedly to put sealant around this vent, but apparently it's not helping.  

We’ve put silicone sealant along the walls of the portion of the house that is affected all the way to the foundation.

I'll definitely keep an eye on that and maybe put a little sealant around the edges.