hyde-
here's the issues. due to the fact that there are specific part numbers for harmonic balancers for the 6.9/7.3 to hook up with specific transmissions, there are some who are nervous on doing a mix-n-match. truth is, these motors are internally balanced design, so they are designed to run whatever you hang off the back of the crank. these motors are not only found in fords but also IH S-series with a dizzying choice of transmissions. Adding to this, wrecking yards will sell you a motor without much regard to what's on the backside and there's really no serious complaints with doing so. If there was, you'd be seeing it here. If I were you I'd install and run with it. If you do have a vibration that troubles you, swap the harmonic balancer.
good luck.