Frusciante used at that time (and still uses most of this gear):
Lots of vintage strats/tele's
Marshall JTM-45
25/55 Silver Jubilee
Marshall Major 200 W
Fender Blackface Showman
Marshall SuperBass 100 W
1 - Moog Expression pedal
2 - MXR Micro Amp
3 - Electro-Harmonix Big Muff Pi USA
4 - Boss DS-2 TurboDistortion
5 - Mosrite FuzzRite
6 - Ibanez WH-10 Wah
7 - Electro-Harmonix Holy Grail Reverb
8 - Moog MF103 12-Stage Phaser
9 - Boss CE-1 Chorus Ensemble
10 - Moog CP-251 Control Processor 11 - Boss FV-50 Volume
12 - Line 6 DL4 Delay Modeler
13 - Electro-Harmonix Deluxe Electric Mistress
14 - DigiTech PDS 1002 Digital Delay
15 - Guyatone VT-X Tube Tremolo
16 - Line 6 FM4 Filter Modeler
17 - Moog MF-101 Low Pass Filter
18 - Moog MF-105B BassMuRF
19 - Moog MF-105 MuRF
20 - Moog MF-102 Ring Mod
And of course: his fingers!