Time for my 2 cents.
The picture that started this mystery is from an article about making califronication from 1999, which can be found in the I-M.net magazine gallery. that is where i found the pic about 1 year ago while making this huge Pedal-Board-History picture which became the basis for Jean's pedal board history from JFTAB. so let's look closer...
That was the article excerpt:
the text says:
Quote
Frusciante's board includes a Boss Chorus Ensemble, an Ibanez WH10 Wah, a Boss FZ-3 Fuzz, a MXR Phase 90 reissue, and a Boss DS-2 Turbo Distortion. To the left of the pedalboard are a Boss DS-1 distortion and another Boss Chorus Ensemble. Stacked behind are a Univibe Stereo Chorus, an Electroharmonix 16-Second Delay, and an Electroharmonix Micro Synth
so either the blue pedal OR the grey pedal has to be the Univibe Stereo Chorus. The other pedal is UNKNOWN.
The point is: there is no point in discussing it, because it is unimportant.
If you are REALLY into musical equipment and gear it's basically interesting to know that most of John's distortion comes from the DS-2, that he uses a WH10 Wah and that he had a Boss Fuzz before the big muff. The big black EHX pedals were only used on ONE SINGLE song (Savior) and weren't used live. And nobody knows what john did with the Univibe and the unknown pedal. It surely wasn't "John's secret weapon that made him sound so good". Professional musicians (especially during the recording of an album) have tons of stuff with them just to have the ability to say "oh, i don't like the sound, let's try it with this thing".
But afterall it is not important. Because the best thing about John is John and not a lifeless metal box with wires in it.
and you should really spend less time looking for John's equipment, because i went through that and all i can say is: It isn't worth it.