My guess is that on a 2006, especially if you have 100k+ miles on it those boots are shot. I just replaced mine for the same reason. You have to take them off, clean them with Brake Clean or something similar and flex them. The cracks become immediately apparent. Mine were perforated all over, but looked fine installed on the truck.
New boots from Ford:
Those prices are from Tousley Ford and can be found online. Any local Ford dealership should be willing to match those prices; mine was.
The new boots are a bit different than the originals. They are orange inside, and have lips to catch the recesses in the metal tube. You have to remove the three staples that hold the band clamp to the boot on the turbo side, as the new one doesn't come with the clamp. Make sure you get a good, consistent union of the boots and the turbo outlet and IC inlet, then tighten those clamps down until snug, followed by torquing them to 9 lbs./ft. (that will seem like a whole lot when tightening them down, but trust me its okay you won't break anything).