Andrew:
Those types of mods are kind of frowned on by the majority of the Pure Stock racers, but they are out there. That's what was so great about Pete certifying...not only did he NOT build the engine to the extremes (per NHRA specs), but he chose not to even blueprint it to Chevrolet extremes (such as deck height, head cc's, etc.). Now, I'm sure there was a LOT of care put into the engine, but like JJ said, he could have done a LOT more. Just imagine what a blueprinted (just to GM specs!) ZL-1 would do! During the "Certified Stock", they had all of the runner specs, and checked everything out
thoroughly. Believe me, they left no stone unturned!
Extrude honing is going on, but at about $400 for a set of exhaust manifolds, you had better be pretty serious. Dave Dudek tested a set on the dyno on his Hemi Challenger, and picked up 12hp (I think) over his non-honed exhausts. I think Brewer had everything that could be honed gone thru, and that engine definitely makes the power.
Stan:
The test you are referring to is, I believe, the test where Bill Porterfield and Batten Performance spun up a ZL-1 on the dyno, trying to simulate the GM tests. But, like you stated, there isn't much info there on the exhaust manifolds

.