I know most of this is old news but some of these bullets seem new to me.
Joe Yoshida posted this at the Gibson Forums today and if Joe posts it, it must all be true.
Hopefully, there's some new info here for everyone. He found it on MF.
2009 R9 Changed Features:
# Nylon 6/6 nut
# Improved ABR-1 bridge (no-wire, tighter tolerances)
# Historically correct nickel-plated brass bridge saddles
# Correct alloy saddle adjustment screws
# Bridge height-adjusting thumbwheels are now thinner
# Neck profile changed - now has less "shoulders"
# Audio taper CTS pots
# '50s wiring
# Pickup routes adjusted so that pickups will be parallel to the strings
# Top carve changed to be closer to several original '59s that were scanned
# Body perimeter change - slightly tighter in waist, cutaway area refined to be more like originals
# The maple cap is very slightly thinner, the mahogany body is very slightly thicker
# The fingerboard is slightly thinner
# The step from neck heel to back of body is taller and more correct
# The taper of the "maple window" under the binding in cutaway is more accurate
# The maple spline (filler strip) in the tenon is more accurate
# The edge radius on the backside of the body is tighter (less rounded)
# The "mustache curve" of the headstock top has been flattened slightly
# The control cavity plate has been relocated, has the correct side taper, and now uses the correct ABS plastic
# The pickguard shape has changed slightly
# The pickguard bracket and screw have been changed
# The truss rod cover has been reshaped to be more accurate
# The serial number location is slightly lower and more correct
# Dial pointers are less sharp
# The strap button screws are longer
# The jack hole is now the correct 1" diameter
# The toggle switch nut has more correct knurled pattern