Disclaimer: I fly fish from a C-Dory, I am far from a Guru, I have much to learn.
Yes, you can fly fish from a C-Dory, but it is not the best of boats for throwing flies. I don't let that stop me! I do keep my boat "clean" on the roofline and in the cockpit because if there is anything a fly line can hook up on. it will. I do 95% of my fly fishing in water where I can see the bottom, or along kelp lines. I use mostly streamer type flies or baitfish patterns for salmon. Most of the salmon that I catch are a late release coho that stay in Puget Sound all year. These fish run about 3 to 5 pounds after a year. Sometimes you can catch blackmouth in the early morning when they come in to feed on herring etc. Not real easy fish to catch. I generally use a 5 or 6 weight rod with a intermediate shooting head line. Either "40 Plus" or Rios "Outbound Express". More and more I have been using a line from Rio called "Deep 7" that is a full sink line. (7 to 8 inches per second) I think it works great around kelp beds.
When the fish are up over 3 to 5 pounds or if the wind is blowing I will go with an 8 weight rod. That is also the rod I would use for targeting steelhead and small kings. (10 to 15 pounds). 12 weight for the big guys, and the folks that I know that fish for tuna off of the coast go even bigger as you can imagine.
Cutthroat fishing is a bit different. I use a 5 weight mostly so that I can get them in quickly to release. I use the same intermediate line, but also a floating line. They usually hold in skinny water and if they are feeding the type of fly is not as important as the strip. They are aggressive feeders. I like to use a popper or gurgler and take them on the surface. You don't get as many hookups, but there is nothing like watching a 20 inch cutt come out of the water after a fly! I use hooks that are size 8 or smaller for cutts as that size is much less likely to do damage to the fish.
As for reels, those made for salt water use are the best, but if you rinse and dry the reel after use, most will do. My favorites are the Lampson Litespeeds. They stand up to salt, and have a great drag system.
Rods, I like a fast action rod because I use the shooting head lines and the wind is usually blowing.
I will post some pictures of flies that I use in my photo album.
Coos Bay looks like a great place to fly fish. There must be returning coho, chinook and steelhead. ???? And it looks like cutthroat country.???
Ocean fly fishing, I know zip. I am planning to go out to Neah Bay with the Brats this summer and do some fly fishing for coho and rockfish. Lots more to learn!!!
Let me know how you do, I think that Coos Bay would be a great C-Dory destination.
Robbi