Aaron, the information I gave out is not just something I made up. It represents the collective wisdom and information gathering of many longtime members of the SC community.
I have read what the manual says and that is what many of us believed for a long time. The newest info about the final balance being put on the engine with pins in the damper and weights on the flywheel or flexplate comes from a retiring Ford engineer who actually worked on the SC and the SC that held the Bonneville speed record for it's class up until a few years ago.
A couple of guys have verified the stock damper is neutral without the pins. Most of the pulleys I have seen have weights welded on them. I do agree that they are the most like part to be out of balance. I have not seen results from someone testing a stock pulley for balance.
I gave out info that they were balanced as a unit for many years. But I don't think that the new sets coming from Ford have any balance pins. I could be wrong, since I have not seen one of those in a looong time. I also think there is a line in the shop manual about moving the pins over to the new balancer which would seem to suggest they balance something other than the damper and pulley.
But the jury is not quite all the way back in the courtroom. LOL Probably the only other way to solve it is to have some balance testing done on several stock dampers and pulleys.
We are considering asking BHJ to add holes to their balancers so the pins could be moved to balance whatever they do actually balance.
But like you said (and others have told me in emails) stock engines at 100,000 miles may be more out of balance by carbon and other deposits than those little pins would weigh.
I believe Ford was concerned with vibration in these V6s made without the counterbalance shaft. From the Ford engineer they did the finally dyanamic balancing with weights on the flywheel and damper. I'm sure the internal engine parts may have been balanced before assembly, so it would not take much to finish the job. That dyanmic balance would include the pulley on the motor, so if it was off, the final balancing would account for that as well.
I'll continue to post more information as it comes in!