For the single-coil tones, Dweezil brings out a mostly stock Eric Johnson signature Strat. In order to quickly move to an acoustic sound, Dweezil installed a bridge with a piezo pickup. He's also playing a prototype of a (hopefully) forthcoming signature model from Gibson. Based off of Frank Zappa's "Roxy"-era SG, it sports a white headstock, a series/parallel switch, and a phase switch–both located on the lower bout.
The heart of Dweezil's tone comes from a Fractal Audio Systems Axe-FX II. In previous versions of his rig he actually ran two units simultaneously due to the CPU demand that his custom presets required. However, on this “Zappa Does Zappa” tour he runs everything through the top unit and the bottom is used as a backup or for any guests that might sit in. In order to recreate his father's famous tones, Dweezil goes back to the master tapes to study and cop every little detail in order to program the Axe-FX II presets.
In order to play incredibly intricate music, each musician in the band is able to control their own monitor mix via a touch-screen tablet along with a Behringer mixer. This allows everyone to adjust on the fly depending on the song and stage volume.
All of Dweezil's effects are run through the front of the Axe-FX II, rather than the effects loop. Along the top is a Bogner Ecstasy Blue, JAM Pedals Fuzz Phrase, SolidGoldFX Formula 76, TC Electronic PolyTune Mini, SolidGoldFX Electroman, JAM Pedals Big Chill Tremolo, and JAM Pedals Red Muck. Along the front of his board is the MFC-101 MIDI Foot Controller for the Axe-FX II and four expression pedals–the first one is for volume and the other three change function depending on the preset.
On the far right side of his pedalboard, Dweezil uses a custom JAM Pedals wah along with an expression pedal to control different variables on his JAM Pedals Big Chill Tremolo. In addition to this wah, he also uses a wah within the Axe-FX II depending on if he wants it before or after his distortion pedals.