Bad vibration!
The early models had near bullet proof lower units; hot forged cranks and Timken bearing on the primary side of the crank. Any crank can be tweaked but the early models are less prone and can take more abuse than the '03 and later cranks.
The first thing you do is take the bike back to the tuner and put him on notice about the vibration and see how he reacts. Most tuners accept no responsibility for whatever happens to your motor once on the dyno but he needs to know that you know he screwed the pooch.
Next step is to open the cam chest, pull the cam plate and check crank runout at the crank pinion; .0015" is typical for the early models. When runout starts to exceed .006".007", you will start to feel the vibration and buzz in the bars and pegs. Once it exceeds .010", you will feel it at lower speeds. Once it gets above .015", everything starts to shake all the time.
If it is the crank, you are looking at pulling the motor, splitting the cases and sending your crank to Hoban Brothers for repair which will include servicing the entire lower unit and truing, balancing and welding the crank. I would send the complete lower unit for them to split, repair and reassemble; I wouldn't leave that for a dealer tech. Hoban will go through the lower unit and replace any bearings or bushings that need replacing and repair the crank. You won't have any worries about crank problems in the future.
If runout checks out, then, as someone has pointed out, the counterbalancers have been damaged. I am not sure but I beleive Hoban can repair them as well and can also lighten them and balance them better than the factory balance. If Hoban doesn't do it, Small Block Charlie does. It will be expensive but you really don't have any choice. I woudl not trust this work to a dealer. Let the dealer do the motor R/R but send the lower unit out for repair.
One last thing, you need to post your dyno results to settle the wager between me and Jeff in your Horsepower!!!!!!! thread. Welcome to the world of Harley performance where **** happens. Let us know how it goes.
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