What can cause muscles pains all over while sleeping that constantly wake me up, i feel like i've exercised throughout the night? had numerous autoimmune testing.

A few things: Muscle cramps can be caused by a few issues, one maybe electrolyte abnormalities, low potassium or magnesium, make sure you are eating a diet rich in various fruits and vegetables to get these. You can also try a magnesium supplement. Another issue could be restless leg syndrome. If your partner notes that you jerk around in your sleep at night this may be the issue. See your doc if so.