Sean
I strongly recommend that you address y/f overgrowth first, particularly if your y/f issues are in the gut. 70% of your immune system resides in your gut, which is severely compromised by the y/f. If left untreated (and w/ lyme tx it will become worse), "leaky gut" develops because of the y/f that damages the mucosal lining of your gut and makes it difficult for your immune system to function properly as well as your digestive system.
The y/f grows "roots" into the mucosal lining, poking holes in it and eventually fecal matter, y/f and other toxins and debris seep out into the blood stream causing severe digestive problems. Your immune system starts reacting to the food particles and you'll eventually develop problems with the food you eat. And the damage to the mucosal lining also prevent you from digesting nutrients properly AND medications/ supplements.
You do NOT want to go down this road, trust me. Most lyme experts say that without a functioning immune system, your body won't ever heal. No medications/herbs can heal lyme w/out the support of the immune system.
Reposted a clickable link Dancingbear* included in her post, this is a pretty good review of the y/f risk and tx:
www.healingwell.com/community/default.aspx?f=30&m=3287783p