Did you consult with an attorney? We're talking about a LOT being at stake here: Most importantly is the potential safety issue which could lead to a loss of life or lives, not to mention certain injury if assembly has flaws or if there are other undetected flaws. Second, you made a significant purchase in good faith from Harley. You don't want a "pig in a poke" after it's all said and done. And have you thought that maybe, even if the bike is repaired correctly, that there will be a diminished value after the repair? A perfectly repaired car has a diminished value due to the fact it was repaired according to most insurance companies.
I wouldn't take another step without consulting a good attorney... As a matter of fact, I would have had an attorney write the letter to Harley. Such a letter would carry a lot more weight and importance. With that said, if I were in your situation, Harley would "eat" your present bike and give me a new one and it would be a 2010. A good attorney would see that you would be taken care of. (Note: No, I'm not an attorney, but I recognize when it's best to use one.)