I have had body aches on and off for 3 weeks. could it have anything to do with coffee?

Probably not: Obviously everything depends on extent, i may feel differently if i find out you were drinking 10 cups of coffee a day, but typically a cup or two of coffee is fairly harmless. It is unlikely to be due to coffee as well if you have been drinking it well longer than 3 weeks. There are so many different causes for body aches it would take a longer doctors visit to get to the bottom of the cause.