Get a pro fit done.

A good fitter will take more measurements than you know what to do with and make the little changes you'll never know you should make. Just for reference, here's some of the numbers from my fitting:

Anatomical Measurements:

Height: 178.8 cm
Inseam: 84.8 cm
Arm span: 178 cm
Torso/Trunk length: 152.2 cm
Forearm length: 35.3 cm
Arm length: both 61 cm
Thighs/Femurs: right, 61.5 cm; left, 61 cm Lower Legs/Tibia: right 56.5 cm; left: 56.8 cm Sternal Notch Height: 149.3 Shoulder Width: 41 cm

Fuji Team '09 56 cm

Center-Top of seat tube collar 56cm
Center-Center Top Tube length 56
Seat tube angle: 73°
Head tube angle: 73.5°
Head tube length: 14.4 cm
Fork offset 45 mm
Trail: 53.8 cm
Stem: 100 mm, with 6° positive rise
Crank length: 172.5 mm
Handlebars: 42 cm (center to center)

Ideal frame geometry:

C-C Seat Tube: 55 (or virtual c-c measure for sloping/compact frame) C-T Seat Tube: 56-57 C-C Top Tube: 55-56 Seat tube angle: 73.50 degrees Head Tube Length: 17-18 cm
Stem: 110 mm
Handlebars: 42 cm
Crank Length: 175

Key measurements for leg extension and torso angles (before / after adjustments):

Knee flexion: right 40° / 35°
Knee flexion: left 40° / 35°
Torso angle, hoods: 40° / 35°
Torso angle, drops 38° / 30°
Torso angle, tops 45° / 44°
Shoulder angle, hoods 93° / 93°

In addition to the minor changes on my bike, he added wedges to both my cleats to compensate for the screwed up rotation of my hips.