I am finding the same! A few weeks ago, I found a 45k mile L96 for $4500, which seemed too expensive, but yesterday, after this thread when I called the guy it had sold for $4500, and another L96 (that looked cleaner and newer) with 90k on it is $4700 - both seemingly from reputable yards.
I am also considering going Gen V 5.3, with an 8-speed and using the H2FA Transfer Case and Torfab adapter. I have discussed the options extensively with Mitch at SwapTime (who is awesome, by the way), and it might make the pain worth it to be able to add an LT version to the LS write-up that DBBowen did, especially with the Gen III and Gen IV motors becoming scarce at reasonable mileages.
With the Gen V, there isn't a way to use the Toyota manual that I have been able to uncover, I would sure love to figure it out though.