26 yo female with severe knee and hand pain in the morning along with pain on balls of feet. pain also in middle of night.possible ra or lyme disease?

Anything is possible: No need to speculate. Go see your family doctor for evaluation, testing & treatment options. S/he can refer you to a rheumatologist if necessary.

Possible: Rheumatology work up is needed, including a discussion with your doctor, as well possible blood tests. There are more than 1 or 2 conditions that could be ruled out on the systemic level.