here is a good example of jerry using both extremes of his middle pickup tone control with and without effects.
3:53 as we rise and fall you can see jerry turn on the effects loop with a Boss Overdrive(yellow box 2nd in rack after the OC2, can be either an OD1 or OD2 and possibly an SD1) i hear him flip the tone control around 4:23'ish also, but don't see him do it.
5:43 just before this bobby flags the change in course and jerry flips off the effects loop. he also flips the tone control back to clean here, but again it is not viewable.
BUT at 5:58 when still clean and no effects, Jerry turns the Tone Control all the way off and at 7:14 turns it all the way back on. at that 7:14 point when he goes from that horn'ish tone to the clean tone we all love, it is very audible and you can visually see him using it.