I honestly believe without a doubt that tire size and pressure is more important than anything else when it comes to vibration and impacts. Played with tire size and pressure for many years to verify this finding, and am sure others have as well. Carbon may have some vibration damping characteristics not available in aluminum or steel, but the correct tire choice very well could save a buyer many shekels! Yesterday we installed 28mm tires on a Caad9 Cannondale which is as wide as it can take and told the owner to run them at 90psi. He came back a few hours later and exclaimed that his problem with bumps and vibration were pretty much solved. He had been running 23mm tires at 100psi.
As for general body discomfort a professional fit may help quite a bit provided the bike can be tweaked to accommodate the fit.