My understanding of the Lyme testing issue is that if you've been infected and then treated with appropriate antibiotics, then the spirochetes are supposed to be dead but apparently leave PCR-detectable bits of themselves laying around indefinitely, meaning that the PCR test can tell you that you did have an infection, but if they've put you through the 2-4 weeks of antibiotics then the PCR test is pretty much useless except as a confirmation that at one point you did have it. A positive PCR test after treatment will not convince anyone that you still have an active infection.
The regular (two-step) tests are supposed to have very good accuracy once you're past the first few weeks of an infection (IIRC).
About 10-20% of patients, and especially those who have experienced symptoms for a period longer than six weeks before treatment, have some degree of lingering symptoms known generally as "Post-Treatment Lyme Disease Syndrome" which behaves rather like an auto-immune response. Most people seem to get better (or at least improve) over time, but some have ongoing problems, which has lead to people who think they have "chronic lyme disease", something that isn't recognized by the medical community generally, but which prompted the movie "Under our Skin" (http://www.underourskin.com/) which is worth watching if you're interested in the subject.
It's a pretty scary disease if just from the ease at which you can get it these days if you live in an area that has a lot of the ticks that carry it (http://www.cdc.gov/lyme/stats/maps/map2010.html). It's been the #1 vector-borne disease in the US for quite a while now. The biggest risk seems to be a long delay before diagnosis as well as many possible incorrect diagnoses (MS, arthritis, etc.)
None of the above is intended to be medical advice of course.
G.
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