Was the contractor licensed? $7 K for that job is highway robbery IMHO. Maybe I've lived in a cow town too long but I can see $1,700 for a licensed guy and $700-1,000 for a handyman, and done right with a new cap. I was in business for myself (electrical contractor) and our success was due to the fact that we did what was in the best interest of the customer. Too many out there now who do everything that is in their own best interest. When you do what is in the customer's best interest word gets out and you have more business than you can handle and you can make a lot of money. Problem today is such a shortage of skilled workers that people who need services are desperate to get anyone that shows up and there are contractors out there taking advantage of this by charging exorbitant rates figuring they will get less work because of the rate but still make good money not having to work as hard.
I'm getting a large 4x8 skylight replaced on a mission tile roof by a licensed guy, includes reflashing with lead and reflashing/sealing the masonry chimney nearby and adding a cricket between the ridge and the skylight curb as the space is only 8" or so, similar to your situation behind the chimney box. Total cost materials and labor = $1,700.
One of the best ways to find a good contractor besides word of mouth is ask around the supply houses where they get their materials, the supply house people usually know who's good and who's a flake. I found my roofer one morning when I was at the roofing supply buying some replacement tiles and overheard him stepping in to help a homeowner who was having issues with work done by someone else.