I quickly found that when sleeping with a mask I had to lie on my back. Since I was sleeping very soundly, this wasn't an issue except that my lower back would scream with pain in the AM and even woke me a few times. I found relief for this by propping up a bit; about 15 degrees I guess. That solved the lower back issue. I know these pains of mine are not generalized but are from lying in a stationary position through the entire night and that might be the key to resolving your pain issue. If you can't come up with a definite reason for the pain, a medical doctor might be a better choice for advice.
The generalized pain in your joints and muscles may not be related to the CPAP therapy and a chat with your doctor seems to be the right answer. My wife suffers fibromyalgia; sometimes here skin is painful to the touch and she has aching in an area that seems to move and sometimes she is OK. I don't think anyone knows what sets this off. She takes meds to help ease the symptoms. I know there are people who have more medical knowledge than I do so hopefully someone can point you in the right direction or t here MAY be a link between CPAP and the pain you have. Keep us apprised of what happens!
This is the sort of info that might prove helpful or at least educational.... google is your friend: http://www.sleep-apnea-guide.com/fibromyalgia-symptoms.html
Only thing I would add is that any article may or may not be accurate even if it sounds scientific.