The process is the same for all Twin Cam engines; remove the rocker covers, rockers, pushrods, and lifters so you can remove the cam chest cover, cam plate, cams, and oil pump. This will expose the pinion shaft of the flywheel assembly (crankshaft). Attach a dial indicator to the engine case such that the plunger is perpendicular to the cam plate bearing surface of the shaft, rotate the crank and record the variation as measured by the dial indicator. For a 1999 to 2006 Twin Cam, acceptable readings will be in the zero to .003" range. For the current junk, acceptable is whatever the crooks in Milwaukee determine it to be after figuring out how much it would cost them to replace all the bad ones. So far that analysis has resulted in changing the max runout tolerance from .003" to .012". I assume when they get their next large batch of junk, the spec tolerance will be changed again to reflect whatever level of crap they have on hand. Makes me want to run right out and buy one.
As for Harley paying to do all of this, don't hold your breath. If there are symptoms that point to a runout problem, Harley may authorize the dealer to do this sort of inspection. However, if you just want to do this because you've heard all the stories and want some peace of mind, sorry but warranty doesn't cover that.
Jerry