Actually Miller I also felt the frame may be a size too small, but the good news is with the seatpost and stem options available, it is really not such a big deal, especially with compact geometry bikes today.

I think your setup looks good, probably too speed oriented for your current level of fitness. Leg extension is fine, reach is fine, back is fine(could always be flat then but your not racing). Maybe you should not change anything, just ride on the bar tops/hoods for another 1000 miles and report back. Or get a cheap adjustable stem for $30 and starting from a higher setting(than current), lower it 1 cm every 200 miles and see where you are at 1000 miles.

Again, I think your setup looks good, problem is most probably a relative lack of biking fitness, and only miles will help.