Sorry for the long read.

Let me first start by saying this issue has been with the bike since the day I bought it new. It has been back to the dealer 3 times, and Ive also had 2 different Indy shops try to work it out. All acknowledge the issue exists, none have been able to diagnose the cause.

Its a bit of a strange issue and hard to describe but Ill do my best...

The motor, for whatever reasons, changes between running super smooth and rough. There doesnt seem to be anything that triggers the change from running smooth to running rough. I have noticed that hard engine breaking will often make it change from rough back to smooth running.

When its running nice, vibes are minimal, really smooth power up when I get on the gas, exhaust note is perfect and zero decel popping.

When its running rough, the engine vibrates excessively, the exhaust has a real loud "banging" note to it, decel popping is loud and nasty.

Even at starting its a coin flip as to how its going to start, smooth or rough. Doesnt seem to matter how it was running when shut down previously.

There doesnt seem to be any power loss when its running rough, none that is noticeable to me at least. If I get on the gas its noisy as heck and vibrates like mad, but still gets up and goes as it should.
At some point i'll shift down for engine breaking and I hear the exhaust note change suddenly and the motor starts running smooth again, like its suddenly found it's happy place. It'll run nice for anywhere between 5 minutes to a couple of hours then its suddenly vibrating and making a racket out the pipes again. Its almost as if the back pressure in the pipes has suddenly increased, you can almost feel each cylinders combustion.

I've been told everything from timing, coil, plugs, fuel, ECM, and almost every other possible cause mentioned. But none of the above when changed out or tweaked has made a single difference. The last visit to the dealer prompted a thorough engine inspection to see if any damage was being caused internally or a cause identified, but a clean bill of health was given.

Its a perplexing problem, one that i fear may cause long term damage, but so far all seems to be in order and no one has been able to work out what is causing this.

open to any and all suggestions, hopefully the collective knowledge here can lead me to identifying the cause.

 

I would check all motor mounts, and intake as well as exhaust leaks

 

Did you check the tank to make sure you don't have something floating around in there that's restricting fuel delivery until you dislodge it under hard deceleration?

 

Pull the ECM connector apart to make sure the pins aren't corroded. They will get a nasty green corrosion if they were ever exposed to water and will cause intermittent runability problems.

 

You do not say anything about codes for Ecm? Does this condition cause the engine
light on speedo to flash or stay on? The popping/ backfire sounds like an injector
wire broken but that would store a code and cause power loss.
Was ECM changed out under warranty? Vibration points to a miss in a cylinder
but again that should cause power loss. So just a wild guess, maybe a lifter
or valve train component is momentarily keeping a valve from closing all the way?
This should show up as a difference in color on one valve. You can take off pipes
and intake to look but it would really show up on the valve heads towards the pistons.
Maybe a bore camera thru the sparkplug hole can see in there?

 

Check the grounds, and battery connections.
If you have a tuner like a PCV disconnect it to check that.
Run some sea foam through it.
Check the header bolts.

 

Check your mods, first.

 

Sounds like an electrical gremlin. Check and recheck wires/connections. Also, sounds like something downstream from the ECU - maybe an injector, as mentioned before. If it was an upstream item, like a loose sensor wire, the ECU would throw a code. Maybe.

It could also be a bad/dirty/corroded injector. Have you tried any STP, MMO or injector cleaner? B12 Chem Tool and MMO are my favorites.

 

Done already, been all over the exhaust several times and double checked after I upgraded from stock to V&H

That I hadnt considered, will check it out

Havent checked this myself will do so.

No codes, no idiot lights flash or light up. ECM changed out 2 times under warranty.

The cylinder missing comment is almost exactly how it feels, but no discernible power loss that you expect with it.

All this done by the dealer and an Indy already.

Problem existed from new and pre mods. Prior to stage 1 the issue was there, the mods have only made it more noticeable.

I've had it in my head that it could be an injector issue, but I've been told they've been pulled and cleaned on one of the dealer visits. Doesnt mean that isnt the problem. Might run some B12 through it anyway.

I've got a few new things to work with, keep 'em coming

 

Karl,

Try the injector cleaner as an additive in a half full tank, ride the bike for some 50 km and see what happens.

After that -like stated previously- check the ecm connector and the injector connectors and clean them with an electrical contact cleaner spray.

When done, spray a little WD40 as a protection.

Anxious to learn if this helps...