Well, if you wouldn't mind reminding me of how you were diagnosed with Lyme? By test or clinically?
Why not make sure that those fungal infections aren't what you are dealing with? I'm a big supporter of making sure that you are treating for the right things!!! It would be fairly easy to make sure that you don't have one of the other conditions you are concerned about
with X-rays of your lungs, "spit" tests, and even blood tests. You would have to be sure that they don't just tell you that you have "an infection" - they need to be specific as you want to rule out those fungal infections.
I lived in Arizona at the time that I had Valley Fever back when I was in high school - like 1979 or 1980 - so I don't really remember too much of it, as Lyme and other infection symptoms were a large part of my life as well - but I do remember taking the anti-fungals since I had an extended course of them at that time. The docs were convinced that Valley Fever treatment would take care of all my issues - nice thought, but of course it didn't work.
The problem is that Lyme likes the lungs of some of us as well, but it's bacterial not fungal. I had severe bronchial infections (always "almost" hospitalized) twice a year for a very long time, so I know what you mean. Fortunately, I've never had a blood clot found though.
And the rash can be from "cat scratch fever" - which is Bartonella - among other things - some of which I have never heard of before!
www.nlm.nih.gov/medlineplus/ency/article/000881.htm