So here is my issue: Brand Spanking new 2013 RGC. Before I took from the dealer I had them instal:
SE Stage IV 103 HO KIT
SE heavy breather
V&H 2 into 1 PRO PIPE Stainless
Ive put 1,000 mile on and it pulls HARD!
However when I have it at idle it makes a slapping sound that I have never heard on any of my other Harley's . Took it back to the Dealer so they could troubleshoot the problem. They came to the conclusion that it was the 58mm throttle bodies butterfly valve banging against the throttle body casing. They ordered a new throttle body and replaced it. Picked up yesterday and it is still making the noise!
All of them pulse in the manifold, with more overlap it gets worse. The TBW throttle body is servo motor controlled and I have heard them do this even on stockers after the Air Cleaner is substituted for an open element type (so this type of thing can be heard unmuffled). I think the Cable TB has more pressure to hold the blade shut so it does not flutter like that, at least that is what I suspect may be the issue, I honestly don't know this 100% for sure.
Not trying to scare you I hope that's what your noise is. ( Not piston slap.)
A simple way to tell is to cover up intake /air cleaner sound should almost go away.
Does it get worse when you are riding?
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As the others said it's most likely reversion, caused by camshafts that actually have overlap(intake and exhaust open at the same time). Scares the crap out alot of folks when they hear it after having an open air filter the first time.
Put the stock air cleaner on it long enough to check, I'll bet the noise goes away.