You may be interested in this discussion of fit. http://sheldonbrown.com/kops.html
I am not in Mr. Bontrager's class when it comes to fitting but I happened on some of the same conclusions about knee-over-pedal not being the best approach. I'm not actively in the business any more but I've roughly used what I could cull from the article in adusting my own fit with good results. Note near the end of the article he contends that even femur length does not necessarily correlate to saddle position.