I am so sorry to read of your discomfort, and I hope I can help you here. Please understand though that online no one can state anything with 100% certainty, all I can do is make my best educated guess based upon what you wrote.
I think it was a wise choice to begin Lyme's disease treatment given the joint pain, fatigue, and you are in a high Lyme's area. Many with Lyme's disease never noticed the classic bulls eye rash, so if you never had one, that does not mean you don't have Lyme's disease.
The CPK is a non specific measure of inflammation. It tells me that somewhere, something in your body is having some type of inflammatory response to something. But it doesn't tell me what and it does not tell me where it is. The RF factor was a good test to run, and I am happy it is negative. It tests for the abnormal protein most often found in rheumatoid arthritis (RA), an autoimmune disease in which the body mistakenly attacks its own systems in the errant "belief" they are invaders. In RA, whats attacked are the joints. Having a negative RF does not rule out autoimmune disorders though.
There is another test called the ANA (antinuclear antibodies) which screens for abnormal proteins found in autoimmune disease. Given your high CPK, if your joint pain continues and you are negative for Lyme's disease, I think it may be wise to talk to your doctor about running this test. If it is positive, further studies called phosphorescence, where the pattern of the proteins are decoded, can tell what autoimmune disease this could be, if it is one.
I liked that your white blood cell counts were normal. (WNL stands for "within normal limits and means nothing abnormal was found or present for that test). These are the cells that help the body fight off infection, and abnormal levels of specific types of WBC can help tell us what the problem might be as each type of WBC is geared to different functions. Your levels were normal, so whatever is happening, it is not affecting your white blood cell count at this time.
Another possible comes to mind. Your sore throat and fatigue makes me wonder if you might possibly have mononucleosis. This is a viral illness caused by the Epstein Barr virus and its hallmarks are the sore throats and usually extreme exhaustion that ensues. Other symptoms can be headache, fevers, skin rashes, nigh sweats. There is a blood test for mono, but there is no treatment for it because it is a virus and not a bacteria. It has to run its course, and typically lasts about four to six weeks. Mono can cause inflammation and enlargement of both the liver and the spleen, which may explain a high CPK. If this is the case, please avoid contact sports or other strenuous acts until your organs are their normal size (can be checked with sonogram/ ultrasound).
More information about mononucleosis is here: http://www.mayoclinic.com/health/mononucleosis/DS00352
I also see you did a heavy work out, (20 squats) and wonder how much of your pain can be attributed to that; but unless you were doing something with your arms at the time, it would not explain the arm pain.
I hope I was able to help, and that you feel better soon,