Dan A said: "that is reasonably affordable (many have taken advantage of the surging demand by raising prices by a lot but that unfortunately won't fit in my budget)." If the current quotes from Miami contractors isn't in your budget, maybe you need to reduce the scope of the project or wait out the market. Contractors in FL got "killed" during the last RE bust, so they are making up for those losses the last 3 years and taking whatever profits the current hot RE market will allow. You don't have to build now and pay current rates ... you can wait for the next RE bust and take "advantage" of a builder!

Your contract should specify a billing rate for the contractor and/or contractor's employees performing work on site. The "contractor's fee" should cover all general and administrative activities, e.g., purchasing, accounting, scheduling, general project coordination, on-site client meetings, progress reporting to the client, etc. If the contractor is performing hands-on work that would otherwise be performed by a trade contractor, I believe it's legitimate for him to charge you for that time.

The counterflashing may not have needed to be replaced; it can last for thousands of years, however, that doesn't mean it's not leaking. I am very skeptical of the saturated chimney brick theory. Sealing brick isn't a good idea, especially if you're in a freeze/thaw cycle area. They charged you for clear floorboards, but bought and installed select floorboards and put the price difference in their pocket. I'd demand the floor you paid for or the difference in the price of the materials refunded.

My brother.