Thanks everyone for the help on the intermittent sumping issue. Harley service says nothing wrong and the company just ignores me.
Luckily, I always stop the bike immediately when it starts running rough- acting like a jackhammer (this happens when the motor is under load, climbing over mountain ranges or driving for more than an hour or so).
An S&S dual scavenging oil pump and a custom re-map for high altitude (screw the warranty) seems to have done the trick.
I'll get the S&S 465 gear driven cam, cam plate, pushrods, metal tappet guides and high capacity tappets put on next month.
After that, I'll take the Screamin eagle intake, and exhaust off and replace it with V&H intake, exhaust and fuel pack.
Then the motor will run like it is supposed to.
Thanks again everyone.