Really dig this video. At the end the camera zooms out and you can see the guitar player's pedals a bit. Looks like mostly boss stuff with maybe a TS9 in there. To me it sounds like an octave down with some overdrive, slapback delay and maybe a boss flanger over it.
I don't hear an octave down...I here some sort of digital pitch shift with modulation. I didn't realize Josh Klingenhoffer was playing with them. Josh is really talented. I love his work on the solo Frusciante albums as well as there other collaborations.
He has used so much gear its hard to guess what it could be, but I think it could easily be approximated with an M9 using some modulation going into the Pitch Glide or something similar.