There was this thread on Lyme testing:
http://forums.phoenixrising.me/index.php?threads/lyme-testing.25260/
Any doctor claiming to a patient that 80% of CFS patients have Lyme is really dodgy, and should not be trusted. There currently no evidence that the 'alternative' testing for Lyme used by some is able to provide any useful information to patients, and the hypothesis that Lyme is a cause of the ill health for a large number of 'CFS' patients who have tested negative with 'mainstream' tests has not picked up any good supporting evidence over the two decades since it was proposed.
At first, this idea may have been plausible and worth exploring (although only as part of research, and with genuinely informed consent), but if it were true that this testing were of value, there should be some good positive evidence for it by now, and there is not.
There is some overlap in symptoms between Lyme and CFS, so it could be worth getting tested, but make sure to use testing that has good evidence to show it's validity, as some of the 'alternative' testing available seems to provide no useful information at all, and can just serve to dump patients with inaccurate diagnoses that lead them to inappropriate treatments (and to lose a lot of time, effort and money).
Best of luck to everyone looking for accurate answers to difficult questions.