Hi Alison!
Welcome to our community! I'm so glad you found us.
If you haven't yet, it would be helpful for you to start with reading through the thread at the top of the forum titled,"New to Lyme?...Start here!!", as it is packed full of important information, symptom lists, helpful links and pdf's, how to detox when one has these infections, information on probiotics and much more. And, here's another good place to find helpful detoxing routines:
http://www.tiredoflyme.com/detox-methods.html
To answer your questions:
1) Yes, there are some people that experience herxing just hours after taking the right medication at the right dosage for these infections.
Yes, what you experience does seem like a herx.
2)Lyme is NOT rare - it's just that few people get diagnosed with it by comparison. It's very common for symptoms to move around or even switch around fairly quickly with Lyme. That's one of the signs that it's actually Lyme.
3)No, 2 weeks of treatment (even though your doctor actually got the dosage right!!!) is not enough. You need to have at least 4 - 6 weeks of treatment. You can take a look at this article - the ILADS treatment guidelines:
www.lymenet.org/BurrGuide200810.pdf I would definitely encourage you to do some detoxing though, as it will lower the severity of your symptoms, even though you said they aren't too bad.
I would encourage you to take the above article to your doctor and see if they will follow those guidelines and give you the full 4 - 6 weeks of treatment.
I would also encourage you to keep reading and asking questions!