The set up will really be dependent on your style and the fishing that you do. The longer the rod, the further you will be able to cast. This is important, but not as important in your kayak because you can get to the fish more easily. You might want more length if you are targeting schools busting or falsies. Also, it will help you reach around the front of the boat or other rods behind you when you get a fish that runs across your bow or stern. For large fish, however, you will need leverage to fight them. The longer the rod, the more leverage advantage the fish has against you. Also, the longer the rod, the more difficult it will be to land the fish. It all depends on what you are willing to give up and what you want. A rod in the 8 foot range should be a good middle ground. I would say the bigger the fish you expect to catch, the shorter the rod you should use from your kayak. I would buy a lower end setup because you might have to adjust based on your needs. Also, kayaking is hard on gear. There is always the chance you will break or lose a rod. Is far as reel goes, get something with a decent drag and corrosion resistance if you can. Line will usually be intermediate or full sinking unless you plan on using a lot of surface flies.
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---------- Post added at 07:48 AM ---------- Previous post was at 07:44 AM ----------
Also, a couple tips for fly fishing in the kayak: keep the deck as clean as possible. Avoid bringing multiple rods. It is always a scramble when you hook a fish and have to decide between losing a fish, losing your rod or losing your paddle. Kayak fly fishing can be a circus. You can troll flies in a kayak until you are use to fighting fish.
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