No I haven't seen any of the special features. I was thinking about watching the alternate ending that you were describing but this sounds interesting too.
I'd recommend any of the special features, but above all else, watch the the "Fear and Loathing on the Road to Hollywood" on disk two, and the deleted scenes on disk one (which includes the alternate ending I mentioned, and my favorite, "The DA from GA" in which Duke and Gonzo make up some bullshit story to scare a DA from Georgia after the Marijuana conference in the Flamingo... The story is absolutely hilarious, and it's a shame it was removed, but if you listen closely to the man on the payphone in the lobby of the Mint, when Duke is checking in and tripping on LSD, he is telling the same exact story).
"Somebody told me when the bomb hits, everybody in a two mile radius will be instantly sublimated, but if you lay face down on the ground for some time, avoiding the residual ripples of heat, you might survive, permanently fucked up and twisted like you're always underwater refracted. But if you do go gas, there's nothing you can do if the air that was once you is mingled and mashed with the kicked up molecules of the enemy's former body. Big-kid-tested, motherf--ker approved."
