06 Fat Boy 88cu in misfiring

I am not a mechanic and I never owned a HD, but logically, if air is coming out of the air cleaner when it misfires, there must be a valve timing problem.

That may have been the cause of your valve problem. From your description, it sounds like it is only the front cylinder. If it has solid lifters, the clearance must be set properly. If it is hydraulic lifters you may have a defective one on the intake valve. It could be that there is a mfg defect with the cam since it has been there from the get go, but that might be a stretch. If a timing chain were off it would affect both cylinders.