could it be an ignition problem!!!!
I've been having the same problem for about 5 months. Bike runs fine going down road until it gets to normal operating temperature then starts lunging and backfiring really bad. If I get it to about 80mph or under 50mph it runs fine. Bike has had the ears taken off and have k&n filters. I also have the silly vacuum petcock open so it's not that. I thought maybe something wrong with carbs but have completely dissasembled and cleaned after this problem, didn't help. Vacuum hoses not kinked. Fuel flows fine out of tank when disconnected, Float level checked, But ran fine for miles and float bowls shouldn't just move anyways, clinked air filter, ran seafoam twice before cleaning carbs, double trippled and quadruple checked carb intake hose and seems tight and solid, vent hoses are not kinked but I sprayed some carb cleaner in through where the vent hose goes just incase something built a home there.
I just don't think it has anything to do with the fuel or air system. Any ideas on anything in the ignition system that could be causing this? I would think that it would be doing it from a start unless it gets warm and starts acting up maybe in the ignitor? But then at high rpm it goes away and don't seem to notice under no load, if I pull in the clutch and rev it doesn't do it.
I'm outa ideas gonna go look at the price of harleys now