It was a tenant rental part of the year, I solely used it part of the year, had someone sharing space for another part.

Is this really happening or is this just a few isolated cases with the news running with this to make landlords look terrible.

In the case I did make some money (I could end up living there for more than 2 years but I just used 2 as an example because that is the shortest amount of time for capital gains primary residence exemption), and say I didn’t claim anything to do with rental properties meaning I solely took in my rent being paid and then paid what I can of my expenses with it, would the capital gains exemption still work as it normally does with a primary residence?

This will go into the overall price you pay for the property and directly effect total CoC, rather than isolate it to the first month.

As Bob mentioned Odoban or an ozone machine are other alternatives if it is a couple isolated areas. 

This also has the advantage that each flip deal you do totally isolates the liability between deals because it has its one LLC.I suppose in theory you could just have the one LLC which both f you are members.

The question is, will it hurt other things around it, or are those things sufficiently isolated in such a way that it won't be a barrier to your operation or that of your neighbors?

I would like one place to track everything while being able to isolate/pull up reports on each property, etc.

So you may have legally isolated the property in a LLC, but you made it easier for somebody to claim an encumbrance exists (should in the off chance one exists).

However, we are in an isolated mountain town and not a socially active area like a beach.