Thanks for all the sound advice. Took the bike in today and spent about an hour and a half just basically refitting. It was almost like rereading this thread, he first plumb bobbed me to check seat to crank position and then started working on my reach. They still have the bike but I think what I will end up with is a zero set back seat post (my knee was about an inch behind the pedal axle even with a forward seat post position) and a little shorter stem (from 110 to around 100 or 90). We lowered me just a little as well (was almost fully extended at 6 oclock). It is great to look at yourself in the camera, they have it set up so you can see your profile in real time as you pedal.

I am really glad I got my first bike with these guys, all these adjustments are being made free of charge even though they are swapping out parts. They really are interested in me being comfortable on the bike and will definitely get my business when I upgrade (which is I guess why they do what they do). My hat is off to them. For those in San Antonio, it is Brittons Bicycle Shop at thousand oaks and 281.