Reddit reviews Kayak: The Animated Manual of Intermediate and Advanced Whitewater Technique

I think most other people will cover the good points. Some are broad topics like food planning and lodging. Some are small topics like not forgetting to sunblock the underside of your chin and watching for bedsores on your ass.

There are two books I consider definitive for what you want to do in terms of paddling: this and this. The first book is for the neophyte who wants to learn as much as possible before setting out on an adventure. The second book is about kayaking rivers and while many techniques will be beyond what you're planning to do, it pays to be aware of the situations that can arise on rivers before you run into them. Kayaking a river is very different from kayaking flat water, and not many books make this distinction very well. I consider both books to be definitive for what they are, and the vast majority of advice I could give you is contained in them.

Also buy the movie "Paddle to Seattle". It's a small independent film- google it and buy it from the guys who made it. It's cheap and is two guys chronicling a trip they made with a lot of similarities to what you're doing.

They rent rafts for the lower Youghiogheny. I've never seen so many paddles just floating down the river! safety boaters were sticking extra raft paddles down their pfds. It seemed lots of people had no clue what they were doing and really needed a guide. Idk maybe it's changed. Upper part is pretty sweet though more like a creek than a river.
New River in WV I believe is higher CFS, meaning cubic feet per second. I met many folks there with little experience, but wanting to learn. Many of the larger outfitters will have trainings for prospective guides. We were allowed to camp on company property.
Many of the guides I knew did not have a raft guide certification, just first aid/CPR. I had one better, wilderness first responder. ACA Swift water rescue is a great class to take.
You should also think about taking a rafting trip as a customer on a few rivers. You will get to talk to the guides and will get great local knowledge. Try calling a few outfitters and tell them your story. They will know where you are coming from bro, was that the AT you hiked? Haha, buy this book, it's about kayakers but it's really great to explain whitewater: http://www.amazon.com/gp/aw/d/0897320506/ref=pd_aw_sims_3?pi=SL500_SY115&simLd=1