Your infection symptoms are quite similar to the respiratory Cpn described in the literature. The body aches are part of the endotoxin/cytokine response suggests two things: that you do indeed have an infection (possibly Cpn) and two, that you have a very high load of bacteria. You should, of course, consult your physician to make sure doxy is appropriate, but it is broad spectrum.
You could well have such a bacterial load that you not only have it in the CNS, the symptoms that you have focused in, but in your respiratory system as well. Hence, you don't have "a cold" but rather are feeling die-off endotoxin and cytokine reactions in your joints, muscles, sinuses, throat, lungs. Remember that Cpn has been implicated in arthritus, fibromyalgia, chronic sinusitus, asthma, and so on. In addition, Cpn infects the immune cells, and makes our immune system less functional in fighting other pathogens.
You need to stay with it, but go very slow if inaddition to the current infection you get a "brisk response" as David Wheldon would call it, to the doxy, and get the support of supplementation.
When you have such a high bacterial load you have to go very cautiously so as not to overwhelm your system. The protocols (see www.CPn Help.org
on the Wheldon, Stratton protocols, and read the Expert comments especially) often describe taking one doxy for the first week, then one every two to three days the next week, then one daily, etc., until the full 100mg twice a day can be reached. Only then is the zithro added in the same way (excepting the full dose may be every other day depending on the protocol).
All of this caution is because of the severe reaction someone who has high bacterial load (I know, I'm one) can have. The longer you've had the infection, the more load you have, the more tissues involved, etc.
And then there are supplements. What are you taking? Stratton doesn't even start anyone on abx until they have countered the secondary porphyria which he now simply assumes as a matter of course, by a month on the recommended supplements. These will really help prevent more oxidative damage which can be caused by endotoxin release in the treatment.
Finally, I've found buffered vitamin C powder, in doses that are just at bowel tolerance (where you do a teaspoon of it every 20minutes until you get diarhea), to help a lot with the endotoxin reactions. Remember to wait until after the doxy for at least an hour, as the magnesium and calcium will prevent it's absorbtion. I found Allergy Research to be the best tolerable form for me. After this first flush, lower the dose below bowel tolerance and find a daily dose that helps but doesn't disturb your bowels.
Hang in there,