I just got Kaliedoscalp and I think that his guitar sound is a mix of his amp and amp simulators. According to his website this is what he uses
What musical equipment does Buckethead use?
Guitars: Jackson Flying V, Steinberger GS, ESP MII, Gibson Chet Atkins, Ibanez X-Series Flying V, Takamine Acoustic, '59 Les Paul Custom (used on some Laswell-related projects), Gibson SG. '69 Gibson Les Paul Custom (used on the Cobra Strike and Viggo Mortensen projects recorded at Travis Dickerson Recording Studio).
Amplifiers: Peavey Reknown, misc. Marshall & Mesa Boogie heads, a Matt Wells head, Harry Kolbe Cabinets.
Effects: Roland SE 50, Rocktron Intellifex, Rockman, a Zoom multi effects unit, Alesis Midiverb II, A wah wah, Lexicon JamMan, Electro Harmonix Micro Synthesizer, Pro Co Rat, Digitech Whammy Pedal, Misc Toys.
Other: Amp Farm amp simulator plug in for Pro Tools (on Cobra Strike)
I think that is a little dated because I know for a fact on the Kaliedoscalp album he uses a Line 6 filter modeler pedal alot...