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When they tuned my bike they got it as close to 13.1 as they could and like I said no more red pipes and the bike runs great. His tune is too lean for his set up.
Check exhaust flanges (and gaskets). Everything might be tight but the gasket could have been pinched funny and caused an air leak. Sometimes you don't see symptoms until its been running for a bit. Might not have shown up during the dyno due to them not running it that long.
Another possibility is the the gaskets seat after the dyno and a few miles riding. Exhaust upgrade 101 says you should come back and re-torque flange bolts to spec 50-100 miles after installation. The exhaust and the engine are moving. The gaskets will seat over time and that leaves a gap.
Another spot to look is the rubber gasket around the intake/EFI coupling. Didn't sound like that was pulled but if so check there too. Either intake or exhaust leaks will produce lean conditions, regardless of the tune.
That's my two cents. Check the simple stuff first before you flame the dealership, the tuner guy, or spend a bunch of money for someone to look the bike over. Worst case you can rule those causes out and narrow the focus on what it actually is.
I have a 07 nightster and my pipes do the same thing,. I also work at a harley shop and all the input i am getting is that sportys run hot and lean to begin with. As long as the pipe is glowing red at the top and not halfway down the pipe we are ok. I would like to hear if anyone else is having this problem also though and what input they have. I have v&h straight shots slip ons with the buckshot heatshields so i can see it through the holes. I just bought a laser temp gun and im going to check the temp of the pipe and engine to see how hot it really is.
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