Hunter S. Thompson and Tom Wolfe (Electric Koolaid Acid Test) are more recent than Kerouac/Ginsberg/Cassady, but their works are of a similar vein.
I'd say there's a different in that Thompson and Wolfe were by far more journalistic than the Beat generation writings. Thompson started out as intending to be a journalist, after all, and quickly realized that he could find more success with the fictionalized first-person accounts of Gonzo Journalism.
Kerouac, Ginsberg, and Cassady, on the other hand, were first writers. It just so happened that their very own lives were probably the most interesting things out there to write about. Kerouac's version of events as Sal Paradise surely differ from reality in many accounts, but it's essentially his "real life" turned into fiction. Ginsberg himself often wrote poems about experiences with Kerouac and "N.C. secret hero of these poems."
As for Naked Lunch, you're thinking of Burroughs there.
And in answer to Pup's question, I'd say yes, definitely change all the names, even your own. For example, in Kerouac's On the Road, Kerouac himself is "Sal Paradise," and his friends Neal Cassady is "Dean Moriarty," and Allen Ginsberg is "Carlo Marx." In Charles Bukowski's novels, he portrays himself through his alter ego "Henry Chinaski."