OH Penny! I'm so sorry to hear of this new issue with your little boy! I had significant issues with my teeth, although they didn't start until I was around 8 or so as I got my infections all on my own.
I came across this though. It's an interview with Dr. Andrew Landerman of California:
www.publichealthalert.org/Articles/marybudinger/lyme%20in%20mouth.htm" MB: Are Lyme bacteria in the teeth?
AL: Not in the enamel, but in the dentin and tubules. Every tooth has some three miles of tiny tubules that spirochetes love to occupy. Antibiotics, even the extended courses that some chronic Lyme patients use, do not get into these tubules. Lyme gravitates toward some teeth. It is my experience that Lyme gravitates especially to the upper and lower centrals, and to the upper and lower first molars. That's eight teeth."
My son was less than a year old when his teeth started abcessing because of chronic ear infections, so my heart goes out to both of you!