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I did do some searching and couldn't find a definitive answer. This is my first Harley..
My bike runs great, no issues with oil pressure, etc
at any time above 2500 I can feel the engine through the bars and the floorboards.
It's not numbing, it's not absurd buts it's there.
Is this normal, or should I start tearing it apart to check run out? I'm really fearful of this crank scissoring thing..
You'd probably be best off to tear it down to check the run out. You're likely going to discover worn timing chain tensioner pads. Unless the engine is super low miles. Once you're in there you should at a minimum upgrade the cam bearings (possibly upgrade the cams and to S&S premium lifters). Upgrade the oil circuit pressure relief spring and plunger (Baisley product). I find with my engine ( 2010 twin cam) that same feeling probably in around the same revs as you're experiencing it. ( I have 45,000 plus miles now) So I find my engine really likes to be in the 29 to 3000 rpm range when cruising at various highway speeds. 5th and 6th gears get the most use. Being that your engine is counterbalanced with a chain driven system there will still be ranges of harmonic vibration. If i recall correctly, just about all the test ride articles back in the day pointed this vibration out.
But if you've got the time, inclination and tools, you could and maybe should tear it down far enough to check your crank pinion run out. You might be surprised that your gut feeling was right. If not continue on with the upgrades suggested above. I think if your crank shows more than 13-15 thou of run out, you've got that serious problem you suspected.
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