The "must have" book for all FE enthusiasts is "How to Rebuild Big-Block Ford Engines" by Steve Christ. Not much on modifying but good for parts identification and building the motor. Most of the modifying info I have is pretty dated but still interesting. "Ford Performance" by Pat Ganahl is fairly good but my copy is dated 1988 so it isn't really cutting edge. Another really interesting book that comes up on ebay now and then is the "HI-PER PARTS" book from ford. It was published in 1968 and has lots of good 428 Cobra Jet information. A little more modern identification info is in "High Performance Ford Engine Parts Interchange" by George Reid. And a couple other I'll mention just because they are on the same shelf are "Engine Bluprinting" by Rick Voegelin and "Chassis Engineering" by Herb Adams.
Beyond that ask questions here and at
http://www.network54.com/Forum/74182
Good luck, I'm anxious to see what other people post to this, good question!
Chuck Brandt