I have an '09 6.0Lx6L80, I still haven't thought up a name for this combo, but am working on it...
Anyway, I don't believe the 6.0 is a flex fuel engine, at least there's no badging saying so. That's actually what was a surprise on mine when I went up north to buy it, as it was advertised as a flex fuel 5.3L, then I noticed the lack of badging, looked under the hood and then asked for the build sheet. The salesman was excited for me. "That's a 6.0L?! Oh that's awesome. 2500 powertrain."
Again, anyway!
The 6.0L I like so far, and if it had the "peppier" 4 spd that'd be even more fun, though it'd be worse mileage. If you could go 6.2L without much of a hassle yeah I'd go that route if you're swapping powertrains anyway.