Still haven't seen an answer as to what is supposedly wrong with the shocks. Are they leaking air, leaking oil, or just worn out? And considering how lousy the stock shocks are, how would you know if they were worn out or not?
Things like shocks and brake pads and other "wear" items aren't usually covered under the warranty or the ESP if they just wear out. Broken seals however would probably still be covered under the ESP; I would ask that dealer to show me in writing if he says it isn't covered, or I would call the administrator of the ESP directly.
Definitely do not buy a replacement set of stock shocks from H-D. Check into Progressive Suspension, Works Performance, etc. for much better shocks. If you want the stock shocks for some reason, get a set on ebay from one of the roughly million folks out there that took the stockers off and upgraded shortly after buying their bikes.
Jerry