I am not a Doctor, but, I have had Carpal Tunnel years ago when I had a job that required a lot of wrist movement. After leaving that job, my condition improved to the point that I do not have the problem anymore.
What you described here, " I spend more time shaking my hands or resting them than i do casting or tying flies", sure sounds like Carpal Tunnel to me and it can be very painful.
Fly fishing and fly tying are two things that I do, and when I am doing them, they are the only 2 things I think about. They clear my mind.