I"ve dinged my V&H several times hopping curbs etc, and have noticed a little more popping on deceleration. The current setup doesn't have any gasket material at all, and I wondered if anyone uses a metal doughnut on theirs for a better seal ?
I've held a candle near the headers and there doesn't appear to be any leaks in sane rpm ranges. Maybe it flexes under load and deceleration ?
On a side note, things are much smoother with a fresh cleaning of the K&N filter today. The stumble around 5,500 rpm is barely noticable anymore. I'm going to start taking better care of it. Maybe flush the filter between oil changes instead of just during oil changes.
There are, and should be, gaskets that go between the exhaust pipe and cylinder heads, they are like a washer but the width is only maybe and 1/8" of an inch. They are made out of alumnium, and often stick quite well to the cylinder head in the bore area for the exhaust, and you have to reach in there and get them loose with your fingernail. Take a flashlight and you should see it.
My guess is if you cleaned your airfilter, and then you heard more popping, then the additional airflow is making it do that? My V&H pipe on the track pops like a mo-fo when decelerating.
There are gaskets that set in the exhaust ports of the engine top. They look like hoop earings. If your bike is old they're covered with soot and hard to see. When I pullled mine out I couldn't even tell they were in there. Looked like part of the engine block. I have a brand new set if you want them for a few bucks.
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Mine has gaskets in there and my V&H pops a lot still. I guess a stage 3, lunchbox and full V&H will do that though.