Hi, first of all, lucky you for scoring that Jamis - I've been lusting after a Quest Elite myself, but can't justify selling my Masi Carbon (yet, that is...). Anyway, as far as the bar being in-line or not-in-line with the axle, everybody sees it a little differently. In my own experience, my Masi came with a 110 stem, and I felt stretched a bit since Masi's have long ETT measures anyway - so I began experimenting and ended up being comfortable with an 80 - 90 stem. I have an 80 on it right now, and coincidently my line of sight has my bars directly over the front axle. Go figure...

One thing to keep in mind: the shorter your stem, the 'quicker', or maybe 'twitchier', your steering is gonna be - so, the closer you get to your steering axis (the steering tube), the more 'on top' of the wheel you're gonna feel. When I went from my stretched out 110 to the 80, I had to get used to the new front end behavior. While you can adjust bikes a lot for your body, there are consequences to your adjustments. I have found the most important measure, once you get a ballpark frame size, is the ETT measure. Once you have that figured out for your body (torso, arms, etc), then further adjustments are made simpler. A good fitter, then, becomes important. You can also research it for yourself and take your own measurements if you are confident....

Hope this helps.