Well, I THINK I can answer at least two of those for you.
I'm fairly sure that you will just need a california fishing license (obtained pretty much anywhere that sells fishing stuff, walmart included).
as for the type of fish you'd be seeing, I would venture to say trout, lots and lots of trout. You may see different types of trout, from rainbow to golden, but I would venture to say you'll be seeing only trout.
I've never hiked the JMT before though, so I'm not sure about where you can fish, I just know I've done a lot of trout fishing in the area over the years.
Asking what the best fishing setup is like asking what the best jacket is, here on the forums. There are going to be a lot of different opinions. Most will probably say a fly fishing setup because thats what they do around here, but I like spinning reels and telescoping rods. You can read a lot about both types here on the fishing forums, and sort of see what the benefits and cons are of each.