I just read this thread and wanted to throw this in. I have never had a tire cup on me in over 120k miles on both a softail (99) and a touring frame (07), Have always used ME880's and about 13k ago a Elite 3 on the 07 rear, both bikes were hopped up with the 07 at 124 hp, and I do push to the limits when riding, the Elite 3 is over 50% tread left.
What I want to mention is I noticed what has been mentioned is everything has been changed or alignment made, but no one has said they changed their shocks or fork internals.
From the get go HD suspension sux period, one thing I know from the auto industry is one of the major causes of tire cupping is too soft or worn out shocks which causes the tires to dribble down the road like a basketball, throw in all the variables and that compounds the issue. Also once a tire starts to cup no matter how slight it gets worse and there is nothing you can do to stop it or slow it down. The same principles apply to the front forks, the most overlooked and untouched item as far as maintenance or a tuning upgrade, I see so many people with 50-60k miles and never changed the fork oil or they go the life of the bike without changing oil (rare but there out there).
Maybe a good suspension tuning upgrade to at least Racetech system or go with Ohlins would be a wise investment, and keep in mind air pressure and load balance is a major key to tire longevity.