Eman -
The guitar in question is a 2005 Les Paul with Tom Short custom PAFs. It's not perfectly quiet, but the phasy sound persists regardless of guitar choice. The sound isn't 'noise' so much as a specific phasing sound during the decay of notes.
My biggest concern is that i DON'T hear this phasing sound in other people's Plexi Variac clips. If i heard it everywhere, I would attribute it to part of the tone. But i only hear it in my clips, and in a few clips from the Avid board. And I'm not looking to get more gain from the Plexi Variac than Van Halen, which it should be able to to produce without a weird phasing sound during the sustain.
Listen to the clip Jimification uploaded last week, and then listen to mine. Same cab and mics. Mine may even have less gain. You'll hear a natural decay on Jimification's clip, and hear a weirdness in mine.