You've done a lot of work to get to the bottom of your problem. Not that the county's word is gospel but if they show you the test results vs. the 'benchmark', you only need to come up with your own conclusion. With their word in lieu of that, I'd tend to believe them. So much for that.
As far as the county's word about the interaction of the 'gases', that is what needs to be done next. Maybe a 2nd visit to the county office to ask for an Air Quality Test, or a reference to a company that does this, is worth the trip. In short, it's what's in the air that you need to have checked out.
As long as the fresh water is 'fresh', I don't see how the plumber could have 'mixed up' any of the lines. (Remember, with all due respect, the county did a water test, or a number of water tests.) The same goes for the glue in the line. I guess I should ask: Did you have the water in the toilet, the hot & cold sink water, the hot and cold shower water, and the MAIN water line tested, or just 1 of these? If the main line was tested, that tells you the water into the house is OK. If the latter 'lines' were tested, they should be as 'clean' as the MAIN water, no? Look into having that done (before the air test) if it wasn't. ALL the end-alls for water should be tested before you spend any more $$$ on an air quality test.
Maybe someone else has some ideas. My best to ya and hope this helps.