Red knuckles along with pain and mild swelling in index and middle finger in both hands, along with feet, knee, and shoulder joint pain on both sides.

Hard to diagnose . Without more history and physical exam, but would recommend you see your physician, have a thorough history and physical and discuss possibility of rheumatoid arthritis. This could be many things, but i would start there. I would also consider asking about infectious causes, such as viral illnesses or lymes disease. Best of luck and i hope this helps.