Scott,
I too wish there were kits available of the brown water navy. The only complete kits I know of are a series of small scale (war game scale, 25mm or smaller) kits.
The closest thing to 1/35 scale kits are the Verlinden LCM3, the Tamiya PBR and the DML LSSC. The old Monogram PCF, RAG boat, and coastal junk, all in 1/48 scale can be found from time to time on ebay and at retailers who specialize in out of production kits.
As for references, there was a Squadron/Signal special on the riverine forces in Viet Nam. I believe this book is now out of print, but you should be able to find one at a used book retailer. The other reference I have is U.S. Small Combatants, by Norman Friedman, published by the Naval Institute Press, IBSN 0-87021-713-5.
If you find other sources for kits or reference please post them and share with the rest of us.