It’s really just a traditional PAF-style humbucker into a clean, chimey Fender amplifier. Sure, there’s some extra dimension thanks to his Fender Super Reverb’s 4x10 cabinet, but that’s mainly felt in the room. At lower volumes and mic’d up, other Fender tube amps like the Princeton or Deluxe would doubtless sound very similar. Those amps just distort earlier, so they can’t stay as clean at band levels. As for the pickups, Jonny may have a vintage Les Paul, but the PAF is probably the most replicated pickup available (certainly the most replicated humbucker). There’s countless guitars and after-market pickups to get that rich, warm sound. Just make sure to play gently. Jonny’s recent style is dramatically soft compared to his playing on The Bends or OK Computer.
From the first concert on Jan 29: Jonny playing his vintage Les Paul in natural finish during the Waving A White Flag. In the background, one can see a cable plugged into Input 1 of the Vibrato channel.
Jonny has a strong preference for to guitars with humbuckers. But Jonny’s other guitars like the Tele Plus and Starcaster have a fairly punchy humbucking sound, with a strong mids presence. In Radiohead, this doubtless helps Jonny to cut through the mix when Thom and Ed are playing. But in The Smile, he doesn’t have to worry about other guitars. So the warmer, slightly mid-scooped sound of a PAF humbucker can shine through. That said, these are fairly minor differences: Jonny’s Les Paul still sounds much closer to his Tele Plus than it does to the trebly jangle of a standard Telecaster’s single coils. The Tele Plus’s Lace Sensor Blue is voiced as a 50s PAF, so the Tele Plus and Les Paul should be especially similar in the neck position.
For the sake of completeness, I should mention that the Boss RE-20’s pre-amp is affecting the tone too. However, it has a fairly minor effect on a guitar’s EQ (it’s more noticeable on keyboards). With his AC30, Jonny would often use the RE20’s pre-amp to boost the signal going into the amp, allowing Jonny to set the amp’s input gain lower to reduce noise. However, at the recent shows he’s kept the volume set at unity gain.
From the first concert on Jan 29: a closeup of Jonny’s pedalboard during Skirting On The Surface. Note the piece of tape indicating unity gain for the Space Echo’s pre-amp.