Guitar pedals to replicate tones in Jefferson Airplane's Surrealistic Pillow? Specifi
 

I have searched all corners of the internet, I have been told an Ampeg Scrambler was used on that album, however that is not the tone I am after. I am not after a fuzz tone. I have also seen that a Vox Tone Bender was used, but again this does not replicate the tones I am specifically after. The best example is in the intro to 'Today', a rather clean tone. Thank you!

I doubt if anyone here is equipped to answer that, maybe go ask Alice, I think she'll know.;)
Jorma Kaukonen played a Gibson ES 345. That model has a "Varitone" switch which uses simple passive circuits consisting of capacitors and inductors to change the tone. I would not have known that unless a hooka smoking caterpillar told me. But yeah maybe the tones you're looking for where from his guitar, and a nice amp. There wasn't much used back then by way of pedals. If any effect was used it might be a clean boost or very slight reverb. e.g. Clapton used a clean boost. James Gurley used a Fender Reverb tank.