Originally Posted by isumano

First, I want to thank V&HBryan for the advice and everyone that contributed to the thread. I hope this will help someone else in the same situation.

The factory took care of it through the Goodwill claim from the dealer. They did not care about the Fuelpack as it can not cause a lift rod to fail. I did not remove it or reflash it. One of the lift rod bottom race bearings failed, and it started a chain reaction that ruined the entire bottom end and damaging the top end. There was metal everywhere, big and small.
Harley factory used the long block program and sent a new engine to the dealer. They covered $6000, which is the long block and some odds and ends needed. I had to pay $3000 for labor and some other odds and ends that were not provided by the factory.
Overall a great experience from the service department, although I wish they had mentioned the Goodwill program themselves instead of making me sweat for a few weeks until I found out about it through here. As soon as I mentioned it, they got working on the claim.

Once again, I hope this thread helps someone in the future that has a similar issue.