Here's my opinion ... but I'm not in the medical field, but I do have Lyme and a co-infection, so take this for what it's worth:
It's a complicated situation to deal with an LLMD on the one hand and a PCP on the other hand, if the PCP is not tuned in to what Lyme is all about. My LLMD insists that patients keep a PCP for the other medical things that come up, but when you tell a PCP about the Lyme treatment, if they disagree with the Lyme protocol, they may not want to get involved at all with any of your medical issues. It's a matter of ethics for them, I suppose.
So hope for the best, and I would suggest you keep your PCP informed briefly of what is going on with your Lyme and treatment, and then move the conversation along to any other non-Lyme medical issues you have. I'm in the situation of not having a PCP anymore, because he was one of those who doesn't believe in Lyme being worth more than 2 weeks of antibiotics. So when I have a sprained ankle or something non-Lyme, I'm kind of stuck. Not good.
Hang in there. Feeling better is worth the hassle, though sometimes it may not seem like it. The depression that can come with Lyme makes it too easy to want to simply give up. Don't go there!! You are not alone.
Many people who are on the same research protocol that I was on have autoimmune diseases, chronic lyme disease and CFS. All of them have intracellular bacteria infections (for more information check out the Health Pages in the fibro / CFS forum) and they all have herxing symptoms.
The Jarisch-Herxheimer reaction (referred to as "Herx" often) is believed to be a reaction caused by organisms (bacteria) dying off and releasing toxins into the body faster than the body may comfortably handle it.
I understand your frustration. I had very bad side effects on doxy and was going to admit myself in to the ER. I contacted my Lyme doc who said to just stop taking them, clear my system of the doxy, and make an appointment.
I was VERY disappointed to say the least as during the time I was off the antibiotics doxy, I acquired new more difficult symptoms.
Now I'm on another brand of doxy and I tolerate it very well so far, but feel I lost two weeks time on my recovery. I haven't increased the dosage yet, so we'll see.
Make sure you take that probiotic in between (at least 2 hours before or after) as some say that is what causes the stomach issue.
Good luck. Patsy's right stick w/ Lyme doc unless you can find a PCP who is open minded.
I plan on looking for one anyways as my Lyme doc is 3 hours away!
I would stick with the lyme doctor. I didn't even discuss it with my PCP. The lyme doctor ran lab tests every other month to make sure all was ok.