My 21 day prescript of doxycycline ended a month ago with no improvement over severe muscle/joint pain I have all over. I am managing just on daily motrin in order to sleep a little and get out of bed but I manage to continue to work OK. I have not been able to keep up my excercise routine like I used to.
Try taking Great Lakes collagen powder every day for the joint and muscle pain (you can get it on amazon), it helps immensely, but you might not see improvement until you've been on it for 30 days. I take 2 tablespoons every day.
Also, clean up your diet - no gluten, no dairy, no sugar.