This is an article which provides some good general information on Lyme disease - Diagnostic Hints and Treatment Guidelines for Lyme and Other Tick Bourne Illnesses. Here are some excerpts:

From Introduction:
To me, "Lyme Disease" is not simply an infection with Borrelia burgdorferi, but a complex illness potentially consisting of multiple tick-derived co-infections. In later stages, it also includes collateral conditions that result from being ill with multiple pathogens, each of which can have profound impact on the person's overall health. Together, damage to virtually all bodily systems can result. In addition, it is possible to see latent infections reactivate, especially viruses of the Herpes type.

From Background Information - General Measures:
Magnesium deficiency is very often present and quite severe. Hyperreflexia, muscle twitches, myocardial irritability, and recurrent tight muscle spasms are clues to this deficiency. Magnesium is predominantly an intracellular ion, so blood level testing is of little value. Oral preparations are acceptable for maintenance, but most need additional, parenteral dosing: 1 gram IV or IM at least once a week until neuromuscular irritability has cleared.

From Lyme Disease Treatment Guidelines - Piroplasmosis (Babesiosis):
Piroplasms are not bacteria, they are protozoans. Therefore, they will not be eradicated by any of the currently used Lyme treatment regimens. Therein lies the significance of coinfections- if a Lyme patient has been extensively treated yet is still ill, suspect a piroplasm.

From Lyme Disease Treatment Guidelines - Course During Therapy

It has been observed that symptoms will flare in cycles every four weeks. It is thought that this represents the organism's cell cycle, with the growth phase occurring once per month. As antibiotics will only kill bacteria during their growth phase, therapy is designed to bracket at least one whole generation cycle. This is why the minimum treatment duration should be at least four weeks. If the antibiotics are working, over time these flares will lessen in severity and duration. The very occurrence of ongoing monthly cycles indicates that living organisms are still present and that antibiotics should be continued.


http://www2.lymenet.org/domino/file.nsf/UID/guidelines

I would like to make one comment. The author of this article observes that "it is possible to see latent infections reactivate, especially viruses of the Herpes type." I wonder if latent infections such as measles and chicken pox could also be reactivated and cause some of the skin rashes that can occur with Lyme disease.