Hello! You’re correct, Jonny is responsible for those noises. He started adding them to the Just intro in 1995, and did so at most performances for the next decade-and-a-half. As is often the case with Jonny, the noise is created with a combination of technique and effects. With his right hand, Jonny scrapes the side of his pick against the grain of his guitar’s wound strings, sliding the pick down the strings for a descent in pitch. With his left, he holds and releases his guitar’s cutoff switch, allowing only short bursts of the noise to be audible (rather than the full descending scrape). As for effects, Jonny uses his Marshall Shredmaster (on its normal settings) and Digitech Whammy. The Whammy is set for a two-octave upward shift with the treadle at max, adding an almost mechanical-sounding warble and instability to the sound. It’s the same instability (and Whammy setting) heard elsewhere on Just, but applied to a percussive noise rather than notes. Ed and Jonny have both used the warble of the Whammy’s one-octave upward shift to great effect (Ed uses it to create the intro sound on Lucky, and Jonny uses it for the main riff on My Iron Lung), but it’s much rarer for the pedal’s particularly unstable two-octave shift to be used. In sum, Jonny takes what is a rather unpleasant scraping sound in isolation, and makes it quite musical using a cutoff switch, a distortion pedal’s harmonics and compression, and a pitch-shifter’s warble.
Close-up video of Jonny at the start of Just is rare, but there’s a very clear view of Jonny performing the technique in this video (0:05-0:07) of the band’s performance of Just at the 1996 Pinkpop Festival. Additionally, you can hear Jonny perform the technique in isolation at the start of this video, from the 2008 Southside Festival.
A screenshot from the Pinkpop performance (youtube). Jonny’s left hand can be seen scraping a pick against the lower wound strings, while his right middle finger rests on the guitar’s cutoff switch.