Ok here is the deal, if your big twin H-D rolled off the factory floor after 2002 your bottom end sucks. The left side bearing in your bike isn't keeping your flywheels where they should be all the time. Call it being cheap, call it planned obsolescence, call it what you will, you need to do something about it before you make any serious run for true power. That means timken bearing upgrade. To do the timken upgrade you have to pull your flywheel assembly.
Even if you are pulling it to go stroker there are some questions you need to seriously consider at that moment. "Is the flywheel assembly I am putting back in my bike going to maximize my riding experience and give me power and reliability?" "Is it just a cookie cutter set some company sells no matter what rpm you ride at most times?" Wait that matters? you ask. Yes it does.
I won't sell a cookie cutter flywheel set to anyone, even if they ask nice. Each and every one is designed for the specific application. Not just stroke length, not just welding, truing or balancing, each set is tailored to the riding style and performance goal of the individual.