Something sounds funny to me. You have a repair manual right, well I would read up and try to figure this out. Just from briefly looking into this problem for you before I remember that there is a way to check if the idle speed control valve is bad or not. You may have to take yours off and test it. If it's bad then order it from www.irontoad.com
and save about 20% off your dealer quoted prices.
I'm not sure what to say about this exactly, testing the ISC valve is a lot of work, but $1000+ is a lot of money to pay to figure something out. It sounds like the dealer has no better idea of what's going on than we do. I've never heard of a MAF going bad hmmm....keep up the research.
Sorry but it has been a long day, TSB=? Also, have you ever cleaned your throttle body? How many miles on your LS?