Can't be much help on the rod but can give you some ideas on a kayak. Personally I would look at a sit on top yak (its what I have so I am a little biased) but they are easy to get in and out of and have lots of storage options. If you are going to be in the bays I would look at something a little longer because it will give you more stability, track better and be a little faster. I have a WS Tarpon 140 and it has worked great for me. There are several people on here that fish out of OK scramblers and the Cobra Fish'n Dive. Another great place for info is the TexasKayakFisherman forum. Most of the people there seem to be Saltwater folks and could probably answer your Kayak questions as well. Be patient, every one on here is usually more than willing to help you out!
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"After all the one place you almost always want to be is on a trout stream with a fly rod. Once you're actually there, it seems unreasonable to impose further conditions."
John Gierach