06'Dyna Street Bob
Stock for almost 34k with no engine mods except suspension and t-bars

So about 2k miles ago at around 34K, I was able to pick up a nice thunderheader for a great price. I slapped it on with plans to have a tune done within the next couple of weeks along with an AC. I noticed the bike developed a weird vibration after a couple of hundred miles that I figured could be possible motor mount failures. It would vibrate like hell while coming to a stop and had a weird vibration at around 70-75mph. I could really feel it through the footpegs but no where else really. At idle I could rev the motor up and feel the dull thud through the pegs. Kinda made me mad that I was going to have to shell out more money on top of the tune.

On my way home from work tonight I was gunning the crap out of the motor trying to pass up a moron weaving in and out of his lane. After shifting into 6th gear and slowing down to about 73mph I noticed the vibration was gone. I then downshifted to 5th and ripped it out to about 90mph and noticed it was super smooth. wtf!?!?!? I came to my exit and notice way less popping and surging to almost non-existent...damn near felt brand new again. And guess what? No ill vibs at all! Thinking something went wrong I ripped it for the next two lights and noticed she was as smooth as glass. Felt like the bike was running perfect.
After arriving home, I noticed the bike wasn't shaking so hard at all. Prior to installing the thunderheader it was shaking quite a bit at idle enough to rattle my brake lever.

Now Im not complaining about this but this is some weird phenomenon to me. I know I really should not have ridden it this way but I pretty much kept it in the rpm range where it was smooth and vib-free. That and my FXR is down for the count and I have no other vehicle. Can anyone explain what the hell just happened? Did I screw something up? Did something fail and the bike is in default mode? There are no engine light or anything out of ordinary. I checked to see if maybe a part was loose the whole time and finally fell off but everything is there. EFI experts? Anyone?!?

 

Gremlins?

 

10 bucks says your pipe is contacting the mid control peg

 

I was going to suggest something similar. As this started after the new pipes, I'd check really closely the clearance all around from the pipes to everything else. Also double check the torque on the mount nuts.

 

I noticed something similar a few times. After about the 3rd time, I realized it was happening after being on a rough cobblestone road. I double checked engine mounts etc and all was good AFTER blasting down the highway... bizarre... but it 'fixed' itself...
gremlins... hahahaa!!!!\

 

Have you at least done a stage 1 high flow air filter to your bike? I ask because you say you have kept it stock. If absolutely nothing is changed except the exhaust, then I don't know how it could run better w/o a stage 1 and tune (but it may not run any worse). In that you do mention decel poping which is generally a sign that your motor is lean, I suspect that either you previously put a high flow air filter on your bike, or you may have had an exhaust leak after you installed your Thunderheader. If an exhaust leak, depending on what you used and how you did the install, I suppose the heat may have sealed the leak. If the problem comes back that is the first thing I would check.

 

There's plenty of clearance between the pipe and footpeg and I know for sure that the I have them torque down correctly. I inspected the pipe to see if there was any rubbing or evidence of contact but nothing. That's where I'm scratching my head. For now I'm putting it out to be gremlins but man, I really would like to know what the heck really happened.

 

Nope never had the money to get into any motor mods until now. I had previously dumped a huge load into the FXR so I went for suspension mods first as handling is always my priority. You mention and exhaust leak that may have sealed its self up. This is entirely possible.

 

Your ECM does self adjust. There is quite the debate about actually whether you require a tuner with stage one or not. "Apparently" if you add exhaust, run the bike, the ECM will self adjust. then after you have put some miles on it and after it adjusts itself, add the intake air flow. The ECM will then re compensate again.
If the bike is now running good, vibrations have disappeared, popping and back firing gone, this is a possibility.
Again, this is a theory and a possibility.