Lots of things do that for me. Grains (most), dairy, legumes, potatoes. I never suspected coffee. Does your son use a lot of dairy products? Maybe in his coffee?

He drinks it black.

He wont touch the stuff now. Been drinking it for ten years.

There could be an indirect link between coffee and achy muscles/joints

Caffeine and other xanthines in coffee (theophylline, theobromine) are diuretic. If he's drinking a lot of coffee (or other caffeinated beverages) in lieu of plain water, there's a possibility he might be chronically dehydrated . Muscle and joint aches can be symptoms of dehydration. In addition, being dehydrated is associated with altered levels of both sodium and potassium .. which can also cause muscle aches and fatigue.

Just a thought

Good point to consider. He,s a one or two mugs a week or month.

I would also check magnesium: that is an important nutrient that can get washed out from coffee's diuretic effect.