I also sell Blue Thunder parts. Having run a set of very well prepped Edelbrocks in the FE that was featured in the July 2004 Hot Rod article, and having recently competed in the Engine Masters Challenge with a Blue Thunder equipped FE - - I have a pretty good feel for the upsides and downsides of both.
The Blue Thunders appear to have a definite advantage as the performance target moves north. The revised plug location and the updated chamber can't really be duplicated without either welding or "porter's special" Edelbrock castings. The advantage does come at the cost of added valvetrain work - and of course the price. I consider the Blue Thunder to have the best potential as a race or near race head. I made 752HP with these on 91 octane.
Edelbrocks are hands down price leaders. The cost is low enough to negate the value of any original heads unless absolute original appearance is mandatory. They have obvious and proven potential in the right hands. I've made right at 700HP with some (OK - only 699). As shipped they are nothing special from a performance perspective - but are excellent "cores" to start out with. Keith has taken them much further in serious race applications.
Shelby stuff appears to fall in a sightly different position than either. They have the cache of the Shelby name, appear to be quite a bit higher performance oriented than the Edelbrock heads are "out of the box". That noted, they don't incorporate the updated characteristics of the Blue Thunders. With moderate potential relative to the cost they are probably best suited for someone who wants a bolt on high performance head.
The one not mentioned in the thread was Dove. They are alternately worshipped and cursed - - sometimes by the same builder - - sometimes in the same sentence. Nobody has developed more iterations of the FE head, nobody has been doing them longer (other than Ford). Many of the fastest FEs in the country have Dove heads. Other Dove heads are holding open doors and propping up shelves - - its been a grab bag - - but to his credit Jim Dove has never quit trying. He was FE when FE wan't cool.
http://www.survivalmotorsports.com/Bluethunderfe.html