40 minute battle?
Also, what is the best way to handle the fish on the flats? I am really worried about releasing a fish that I just spent forty minutes fighting(hopefully).
Ricky-
You have gotten some good advice. A nine wt and 350 line will be a good match for the flats and much of the bay. You do not need a 10 wt to land stripers but may want one later to toss really big flies.
I have caught fish on the fly in the flats to 38 pounds and it took less than five minutes to land any of the larger fish with a nine wt. On bigger fish keep your rod at a low angle (10 o'clock) with the drag set at fairly light as he takes his first run. Palm the reel to apply extra pressure. Once you know your reel better, you can tighten it slightly. The fish in the flats will not run very far. If the fish is large and you have a bud on the boat, let him assist with the landing.
There is no need to use light tippet, if not fishing for records. I like to use leader and tippet that is just under the breaking strength of the flyline. 25 pound FC is what I normally use. I would use 30 but if you get hung up and need to pop the fly off, the sinking part of the flyline may break. Heavier leader and tippet make landing much easier and more certain. Just lead the fish to your bud and let him grab the line and lip the fish. Boga grips are OK but strong thumbs are more certain--one thumb for fish up to 20 pounds and two thumbs for bigger ones. I do not like to net fish that are to be released.
If you catch a fish that takes you 40 minutes to land, it would be in the 60 pound range or bigger. I have not heard of fish over about 55 pounds caught up there and they were not on a fly. A fly rod is a much more efficient tool than believed. It amazes me how quickly fish tire with a 9' fly rod.
Good luck.