preliminary results
As mentioned previously, I wrote a lineup simulator in C to run through all 9! permutations. I tested it against the 2005 Astros. The full results are here (6.8 MB gzipped text file), but here are the top 10 and bottom 10 lineups.
The classic lineup:
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This lineup clocks in about 1 run per game lower than was actually scored last year. Part of this probably is due to not accounting for steals, defensive errors, or sacrifices.
Top 10:

Bottom 10:

For reference, here's the output from the Baseball Musings lineup analysis tool.
Surprisingly, my simulator strongly suggests loading all of your best hitters up front. The leadoff position suggests putting someone with a good OBA (as you would expect) and then straight away putting your best two sluggers in the next slots. There also seems to be some support for the second leadoff batter theory here as well, with Taveras in the 9 hole. At best, the non-traditional lineup nets me about 12 runs on the season over the classic lineup. That's maybe one win. The differential between the best and worst possible lineups is pretty significant, around 10%.
One thing to consider; NL numbers might not be the best numbers to test this on because there are a lot of double switches in the back third of many games when relievers are brought in which changes lineups considerably. My next run, I think I'm going to take aggregated numbers for AL lineups.
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I love this kinda shit. Anyway, there has to be some serious problem with your simulation, because as you noted your run scoring is way too low. There's no way omitting steals, errors, and sacrifices can cut scoring almost 25%. I'm not really sure what the problem is though.
I've read some of Cyril Morong's shit before...I don't think much of him as a sabermetrician. Or as a writer. However, The Book, discussed in that Hardball Times article, is quality shit. I've been reading things by Tangotiger for a few years and he is absolutely brilliant. The Book's chapter on lineup construction does confirm the validity of the "2nd leadoff hitter" strategy. Tony LaRussa batted his pitcher 8th a little bit a few years ago
It would be interesting to see what your model projects should be the best lineup for Houston in 2006. For instance, Ausmus is not gonna put up a .351 OBP again, so he shouldn't really be leading off. Of course, this depends on what projections you use. If you are interested you could try these: http://www.baseballthinkfactory.org/files/oracle/discussion/2006_zips_projections_houston_astros/