Buckethead had the coop but you can see in the extras for the first Brain DVD that it's basically a rehearsal room with all the gear set up and a wire fence put around it, nothing you'd look at and say was halting production or causing shit.
when the Zutaut leaks happened I was convinced then and i'm still convinced now you could/they should have made a great album out of the rough mixes on the first four CDs, a version of CD with Perhaps and Atlas in place of stuff like Scraped would have been it, man. Like that's the stuff I was hearing in my head when Axl spoke about an abums worth of music with a bonus disc of other shit, with that line up once Fortus settled in. Way before Better, way before they had the chance to add anything else