What you want is a solid, local roofing contractor who has the GAF Master Elite Factory Certification. These contractors will not be much more expensive than others in the area, and will be making sure all your flashing, etc. is done to the highest level of quality.
They don't screw around with cutting corners anywhere because once they earn that Factory Elite certification, they don't want to lose it.
Here's the website of the contractor that did our reroof a few years ago... nothing flashy as far as sites go, but informational. He came highly recommended and was top notch. Explained everything and answered all my questions.
Burgin Roofing
GAF website... lots of info there and you can punch in your zipcode and find certified contractors in your area:
GAF Materials Corporation | Roofing
No, I don't own stock in GAF, I was just very impressed by this guy.