Some things I know about FZ's sound:
He sometimes used a Barcus Berry contact transducer in the neck of his guitars, this allowed him to have the sound of the plectrum mixed with the pups.
He used a pignose amp in the studio (as can be seen from the DZ video mentioned above). That active circuitry did a lot for the sound - amazing.
He also used Marshall 100w heads and JBL equipped cabs (no other detail)
He used metal picks (latterly) and liked to tap the nick with his pick sometimes. I have heard that chap out of the Meat Puppets so something similar. It is a sort of tapping thing but sounds a bit weirder. Plus FZ used to pluck at his strings with his pick (imagine pulling a hair with your thumb and 1st finger). Get "Does Humor Belong in Music" on EMI DVD and you will see his technique up close.
Here is an extract from an article I saved ages ago - I can't find the link anymore:
Frank Zappa played two custom Strats on the Broadway the Hardway tour. One was the blonde-finished instrument that also appears on much of the Guitar LP. It consists of a heavy Fender Stratocaster body, a custom neck made by Performance Guitar, a Floyd Rose tailpiece and Seymour Duncan pickups wound for an 8-k boost. Strings are Ernie Ball Stainless Steels.
Except for its lighter-weight body and dark brown finish, the other Strat is virtually the same. Both axes include a custom active electronics circuit developed right at Zappa's Utility Muffin Research Kitchen.
"It's got a gain stage and two parametric EQ circuits built into it," Frank explains. "The pots give you variable frequency selection and variable boost/cut at different frequencies. And then there's a screwdriver adjustment for the Q of the filter. That allows you to tune right into the feedback point of any room so you can really control what you're doing with feedback."
On tour, the guitars went through a pair of Carvin heads and a Roland GP-8 effects processor for Zappa's clean sound. His dirty sound was provided by four Marshall heads: 200 and 250W. Most of the speaker cabinets for these heads were placed and miked beneath the stage for better isolation. In addition, Zappa used a single 50W Marshall head and cabinet for onstage monitoring of his distorto sound.
