I didn't mean to publish this drafty fragment. It published itself. IIWII.
Russian River connection might have to do with them spending time at the Warnecke Ranch out on Chalk Hill Rd in Healdsburg. Alligator was supposed to be written there.
7/16/67 interview Garcia says they are looking to move to the Southwest, with specific mention of New Mexico. I would be stunned if this were not connected with Hunter.
Here's what The Bard says in Box of Rain (1):
This was one of my first lyrics recorded by the Dead. I got paid two hundred fifty dollars from the record advance for Anthem of the Sun with which I bought a used car and headed north to Seattle, where I tried to make a living restringing beads from Goodwill for a friend's boutique. I made about five dollars at this occupation. The car broke down, which was okay, since I couldn't afford gas for it, so I hitchhiked back to S.F. and decided to hang out there with the Dead.
Dodd (2) doesn't say much about the near origins of the song (i.e., through any Hunter biography), but has characteristically brilliant and fascinating analysis of its various historical progenitors and other relatives.
(1) Hunter, Robert. 1990. A Box of Rain: Collected Lyrics of Robert Hunter. New York: Viking Press (s.v. "Alligator", pp. 6-7).
(2) Dodd, David, ed. 2005. The Complete Annotated Grateful Dead Lyrics, annotations by David Dodd, Foreword by Robert Hunter. New York: Free Press (s.v. "Alligator", pp. 36-38).