What has happened to my wonderful smooth bike?

I have had my TR for just over a year.
For the majority of that time this has been a wonderful smooth bike.
Over the past month it has become more vibey & surgey

I never had any stalling issues, but did add a Wuka booster/spoofer after a few months that generally made the bike better to ride.
However in the past month+ the bike really began running poorly.
Stumbles, stalls, became more vibey and had issues with surging.

I did the ECU power down/reset with the wuka in place and it really ran bad, lots of stalling.
Re-did the reset with the wuka removed, and then re-installed it.
The stalling issues went away but the vibes and surging are still present, maybe even a bit worse.

Funny, i just started having the same issues. Was on my way home sunday after a ride, doing about 55 and i felt the power go away a few times. Never died completely, little twist of the throttle and all was well. When i went to work Monday morning was no more then 1/4 mile from house and she started coughing and running rough. Turned around and took it home.just got home from work and was going to start going through the basics.
Looking through the manual and here no mention of a fuel filter except an in tank one. Is that the only fuel filter?

I have a pre-filter and a grease sealed main filter.
I have around 5000 miles and was hoping it was not really due for check/adjustment yet.

In the middle of the reset now, air filter and box clean as can be. Don't do much dirt riding.

It's conceivable that your valves need adjusting however, my Eruption mod was learned by the ECU in about 1k after which all the issues returned. At 3K + I installed the AF-XIED device and the bike has run perfect ever since. The Wuka and Eruption are air temperature spoofers and the Magnetti Marelli ECU quickly reverts back the OEM fuel map (some experience change, and others like High Five are still happy with the Wuka).

The XIED is an o2 spoofer. The ECU is always sampling from the o2 sensor. It looks for electronic signals to adjust the AF settings (Air Fuel). Since it has to change and adapt to the o2 readings on the fly the ECU cannot learn and revert back to the OEM settings as there are none. What the XIED device does is tell the ECU that it needs to inject more fuel. What this does is stop the lean condition across the board by injecting more fuel. You can set it from about 3% to 8% richer. My engine is smooth as silk now, no vibes, shifts easier because it gets to rpm quicker, it has more torque across the board, it has cured the snatchy throttle, and made the exhaust note richer and deeper in tone. The downside of course is that you use more fuel. I will continue using XIED until and unless someone breaks the hex codes so we can understand our ECU's and hopefully be able to remap them.

This seems too sudden and notable a change to me to be valves, but perhaps.
Oddly my only experience with out of spec valves was with my KTM 640 and putting it back in spec made it more vibey.

FWIW My bike ran well on the Wuka for at least 4000 miles.

I have to say I am in the wait and see mode on any other gizmos with this bike.
The spoofers were the answer for quite a while, now they are crap.

Ogre_fl This is what I was talking about a little while ago myself. I have had the valves checked, changed oil religiously, changed air filter and used grease to help seal it, added different hand grips and the anti vibe 2" rox riser has helped some. But the smoothness is gone. Next up is front tire change. I have approximate 10k miles now. I have rode it in the dirt once and not a lot of dust in the air. 99.999% on road in good air conditions. My 1 year warranty is out in the end of august so changing the front tire and bearings is the last resort. Although it is to me more in the motor when you get into the throttle. Some is out of throttle maybe front tire and bad bearings. After that I am clueless. I have no spoofer and was going to install pcv with auto tune as I see the only way to keep the bike rich enough. If I can not get the roughness out I will be parking this as a daily and getting the KTM 1190 adventure r for daily. I am hoping some one else has had these problems with vibration and can chime in too.

Riding Again,
I remember you saying you had issues with vibes and I did not understand it.
At that time mine was still running silky smooth.
Now I have to say I understand.

Mine is the motor or drive and as you note its particularly bad under throttle.
I want to believe it is a heat/humidity related to the fueling thing.
However, last year at this time the bike was silky smooth.
I also would have thought some of the Aussie guys would have had similar issues during their summer months.

Question, do you still have the stock chain?

Mine seems like the fuel supply. Reset did not help. Next step is unplug the Booster plug and see if that is the culprit.
Any reason not to run some injector cleaner thru the gas? It mainly looses power when i am just traveking at a constant speed. A little turn of the throttle and it comes back to life.

Yeah! My bike is not liking the hot and humid florida weather also. I run the wuka also....17700 miles and this is what the air box looked like. I had 5/8 oiled pre-filter in front of paper and silicone also. Now i just run a homemade uni 5/8 doubled layer with old paper filter gasket on it. Air box not that dirty but throttle-body is a little oily..to much uni-oil or valves maybe! Dealer did the valve check and said ok! Need air box fix now:-)

You might want to check the torque on the motor mount bolts. If they're a bit under torqued it can have quite a dramatic effect on vibration. I recently retorqued my Strada and found several that were below spec.

I second this motion. Ogre, I've got a bit more miles on mine than you do, and I haven't experienced this vibration at all. I don't think there is a EFI ghost to worry about here. I suspect something basic in your setup is wrong. As we say in networking, verify your physical layer first. Check your bolts, engine mounts, and anything where parts connect.

Your throttle body does not look that bad to me.
My X-Challenge looked about like that at 3,000 miles.
They had issues with the crank case venting getting in the idle actuator and gumming it up. The air filter did not seal that well either.
It was pretty common for the air box and throttle body to be oily.

Thanks guys, checking the torques was the first thing I did.
I have even removed the skid plate and crash bars to eliminate their effects from the equation.

When Riding Again mentioned issues with vibes a while back I did not understand it either as mine had been very smooth.

Ogre_fl I do have a new xw chain installed when I did the rear tire and valve check.

I do not think the heat has any thing to do with it. Mine has been acting this way when it was cold as well. In fact first time I started noticing was about the 4-5k mile mark in February while it was still cold. I have checked all the bolts for proper torque as well. I believe it is inside the motor. Like a bad bearing or spun bearing. I have done 7 oil changes to 7200 miles and about to do my 8th at 10,200 miles. I could not see it being due to improper or dirty oil. I do about 300 miles a week. I checked my paper work and I bought mine 8/20/13 and will be taking it to the ktm dealer in jax. I do not trust the dealer in Orlando. They forgot to torque down my rear axle and luckily after an hour and half ride home I checked it and noticed the wheel moved easily. Nut could be tightened by hand. LOL I am already skeptical of any one doing work on anything I own and that happens. To me now every thing else they did is compromised. Although I have went over every thing again myself since then.

Just came across this thread LOOSE. I am going to check the fuel injector and change spark plugs shortly and see if this is the issue.

I didn't get a tool kit with bike....but after i find that spark-plug wrench i will change plugs also. Could not hurt...i am at 17800 miles.

Did you guys ever solve this?

For me, new spark plugs did the trick.
Actually just re-gaping the original plugs got it pretty much back, but the new plugs did seem to make for a slight further improvement.