Ahh, the good old free-floater.
Turns out that the guy who picked up Chamberlin's Zeitgeist kit also got a hold of the [missing] part of Jimmy's Gish era kit at the same place...
According to Mekong56, the store, who contacted Jimmy, explained that the snare was used both to tour subsequent to the release of Gish and on the album itself. Read the rest of this story over at the Pearl Drummers Forum.
In other news, good old, Billy Corgan, mentions in a new video interview that he is still working on releasing a Gish Box Set to celebrate the album's 20th anniversary (next year). But there's only one thing stopping it now. The evil fat cats at EMI aren't letting him do it. So, he's asked for some help - go show you support for the project here. Seriously, please do.