One of the ways he got caught was a fuckup on his part. He claimed a really high speed run of Through the Fire and Flames, and ended up taking the video down claiming copyright. This ended up being bunk, because someone saved the video while it was up and it turned out that he spliced in such a way as to "lose" something like 2,000 points mid-song. Guitar Hero has never had any mechanic to allow one to lose points they had already gained (unless it did in the earliest GH1 development days). The only thing even remotely close to that is the Big Rock Endings from the Rock Band series, where you have a series of freeform lanes to do whatever you want in order to build up a bonus, which is subsequently awarded to your actual score when you hit the final few gems after the BRE. But, those points aren't tallied to your total score until you actually hit the final gems. The score discrepancy in Schmooey's TTFAF video was a decrease in the actual score, as Clone Hero doesn't support Rock Band style BREs.
It is literally impossible to have that happen legitimately, and that's why he took the video down, because it essentially was a key component of what busted him (and was also featured in the Jobst documentary).