I thought this was a really good post. Not that I agree, etc., but a very meaningful contribution.
Lots o questions. Just start w/ a couple:
1) How did he "sidestep the biochemical utilization of energy to produce work"? It seems to me that he was emphasizing that in the SLoT equations you have to balance "statistical entropy" or whatever we're calling it and "thermal entropy" independently (amongst other things). Are you just saying that you don't think his thermal equations were complete because his system was not complete?
2) You said "his understanding of evolution and biology is quite poor, as evidenced by his use of a slightly modified tornada in a junkyard analogy". Why does this make his understanding of evo/bio poor? Because the process is presumed to be far more gradualistic than that? As I remember it, thermodynamics doesn't care too much about the path you take from energy state A to energy state B; if it's uphill, then even if you divide the path into infinitessimally small uphill gradations, you still have to travel that same thermal/entropic ladder.
(Caveat: I did learn all this stuff quite extensively once upon a time, but I really need to brush up on the details, so I may be talking cr@p here.)
I'll give your questions a shot sometime tomorrow. As long as my brain works.