I feel your pain, but the failure wasn't necessarily due to using the stock lifters versus the SE lifters. Both have suffered the same failure you mentioned, and in fact there is a recent thread on the site about the SE lifters in a 120R engine that did the exact same thing at very low mileage.
Any time you make internal modifications to the engine, other than the street legal kits Harley sells, even if you use a Harley kit and have a Harley dealer install it you will find that Harley can and will void the warranty. The literature and advertising for those stage 2,3, or 4 kits actually mention that. The dealer should have also mentioned it, but few do and some even BS the customers and tell them it will still be covered just to make a sale.
If your dealer lead you to believe the modifications wouldn't affect the warranty, they are the ones who need to stand up and help with the problem.
Jerry