I have a "how to build 2004r" video very basic though it is nice if you never done one for referencing to, also ATSG, Haynes and GM service manuals all of which are a big help if you know what you are doing to begin with. The biggest help for performance has been "Strengthing The 200 4r" article and this board itself. Like Bruce said "Be CLEAN and take your time" very small articles of debris can cause hugh unknown problems, also it took me 6 months of research and parts acquisition and help from here to start and finish my rebuild and it was well worth the wait to have what I have know. As far as parts you won't find any better than what you will get from "PTS" and like Bruce said the customer serivce is the best bar nun. TCI also has good stuff as well but are somewhat limited on what they offer but what they do have is good.
As for the difference from the run of the mill 2004r and the performance ones are: Basics- valve body, govenor and servo. To tell you what the vb differeces are would be beyond the scope of this, regular can be modified but you would have to send it to Bruce or buy one out right for about $500 I think, the gov. is for different shift points also can be easily modified to your preferance and the servo is larger for better 2nd gear holding but most go with an even larger billet servo to accomidate more performance. If you are interested in a good core you want a BR, BQ, CZ, KZ, OZ TA all will be a good starting one. If you do enough searching on here you find most of what you need but don't hesitate to ask. The parts Bruce sells and the ones he builds far exceed the performance of a BRF and all the mods are for performance and also durability. The main thing is the vb if you can acuire one of the listed one's or even just the vb everthing else can be purchased or modified to meet and beat the stock BRF.
. I can offer you an ATSG manual which I stock for reference purposes. Also I can also offer you guidence and the correct quality parts to do a very nice job. 
