What a lousy problem to have with a new bike. As for the letter, if it's been sent already there isn't much reason to comment.
Why not phone HD corporate? You can probably get a person to call if you ask the dealer and go up the MOCO foodchain till you find a satisfactory solution.
You might consider making the following points:
1. While the MOCO is accepting responsibility, the right solution is to replace you Ultra because: (a) the bike should never have left York in the first place; (b) bikes needing a frame replacement usually involve an accident are usually "totalled" and dealership service personnel, therefore, almost never have to do a total bike disassembly/reassembly; (c) it's unrealistic to expect that the bike can be reassembled in a dealership with the same skill and precision (torqued fasteners, electrical lines run and secured, etc.) as it would be on initial assembly at the factory; (d) warranty repairs are typically assigned to the least experienced tech and MOCO reimbursement to the dealership is at below retail rates for the labor; (e) the Ultra is the most complex (features and associated components and wiring) bike sold by MOCO increasing the probability that it won't be assembled correctly; and, (f) the bike's normal fair market value has been severely diminished by the above.
IMO, spending time talking or writing about MOCO "support" for San Jose HD and extending the 2-year warranty for the replacement frame and swingarm BEFORE making the points for a new, replacement Ultra diminishes your effort to get what you really want which is a new Ultra. Besides, the warranty is the MOCO's responsibility, not the dealership's, and an HD store is going to be tasked with doing warranty repair work regardless of who owns the store.
Hope you resolve this to your satisfaction.