There is a video called"rebuilding the 200-4r" from Technical Video in Wisconsin. It covers a basic stock rebuild. I bought a copy and learned enough to be dangerous. Chris Kokkonis (chris718) is publishing a book which I'm sure will be some of the best info in print when it's released, search down for the thread. Other than that, ATSG and Haynes also publish rebuild manuals. Good luck.
I found a 2004R service manual on Ebay from ATSG. They have manuals for every kind of transmission you can think of. Just go to transmissions and type in the kind of transmission you are working on and they should come up.