My brother bought the Trek Fuel EX 8 about 3 months ago and the only thing he grumbles about is the Avid Juicy 5 brakes. They are a pain to setup. I gave him some tips and they worked great so here they are, I hope they help you.

First, don't squeeze the brakes with the wheel out of the dropouts- it extends the pistons with no resistance and they don't retract back equally to put the rotor in the gap in the middle. If you do, or if you need to 'reset' it to center the calipers, remove the wheels, and using a 10mm wrench, carefully compress both pistons all the way, then reinstall the wheel and squeeze the brakes.

The brake rub issue may also be due to the brake pads not being parallel to the rotor. To adjust them after loosening the two bolts, use a feeler gauge (sorry I don't know the proper gap off of the top of my noggin). They can be had from an auto parts store (not the little wire gappers good for sparkplugs, but gauges that look like Popsicle sticks of varying thickness). Insert one in the gap between the outer brake and rotor, push the brake body against it, then tighten the bolts. (I would do this after centering the pistons as mentioned in paragraph 2)

The bolts that secure the brakes have concave and convex washers installed in them in order to provide some movement for adjustment but the problem is if the brakes are not held in a stable way (with a gauge), they can pivot and move as you tighten them and that can cause all kinds of grief until the brakes are held in place.