I've had periodic body/joint/head aches, chills, sweating and a low fever for 3 yrs now, what could this be?

Various causes. List of possibilities can be a bit scary; before reading on, keep in mind that periodic symptoms can be from unrelated seasonal viral infections. Other possibilities: infection (eg. Tb), auto-immune disease (rheumatoid arthritis, lupus), vasculitis (blood vessel inflammation), endocarditis (infection of heart valve), immune deficiency (hiv, bone marrow). Well worthwhile getting a check-up.
Go to MD now. Any medical problem lasting this long needs investigation. You need to visit your physician now, and get whatever tests they prescribe. It's been three years, don't dabble with this any longer.