B1100 new engine vibration after stepper bypass

[LeakyLogic]

I figured I'd see if plugging the hose to stepper motor could eliminate the popping on overun and it did. However, the bike runs completely different and that is all I changed. There seems to be some constant vibration coming from the engine, like that from a four stroke dirt bike, but not as severe.
Recently I did the valves, sync throttle bodies new fluids and plugs, fuel filter and air filter.
I am running 2230bd00 1200 2v non ABS map with lambda AKA O2 sensor on. Perhaps I should try 2230bd01 because if I recall the ignition was advanced and see how that does. Before that I'll double check the throttle bodies and see if they are still synced.
I do not find the vibration uncomfortable, but I am concerned it is detonating the fuel at the wrong time and could cause harm to the engine.
Throttle response had improved and is excellent at low to mid range with a noticeable increase in torque simply by plugging the stepper hose going to the air filter. It does not like to rev as much as before above 7k rpm, but I'm rarely in that range.
Overall, I guess I have to decide if some burble on decel and a little less torque is better than more torque and some possible damaging vibrations.
Also, I lost a nut on my shifter linkage during that test ride.

[derek533]

My B1100 vibrates as well.  I had just assumed it was because I was short shifting before the engine could get into its RPM sweet spot between 3500-4000 rpms before smoothing out.  Even when it does smooth out, there is still some vibes that you can feel but they aren't bad at all and no where near what I would call uncomfortable. 

[LeakyLogic]

I try to not lug it and keep the rpm above 3500. This vibration seems across the entire rev range. It is different than previous tunes. I kind of like it. Nice power but a totally different personality than before. Tommorow, I will double check the TB sync and see if it calms the vibes down a little bit.

[pete roper]

You have checked the TPS and cleared the trims?

Pete

[LeakyLogic]

I wonder if having the O2 sensor on and stepper motor off is an oxymoron, so I will turn off the sensor. Reset TPS and Learning parameters. Warm up past 60c and adjust CO trim for smooth idle. Shut down engine and Loosen throttle cable and clean throttle stop. Balance TBs at 4K. Shut down motor with kill switch. Reset TPS again. Start engine again and set idle balance and double check TB sync. Retighten throttle play. Then go for a ride and see.

[LeakyLogic]

It seems all it needed was a proper TB sync. With the O2 sensor on and stepper motor plugged it runs the best I had it running since I purchased the bike, which was in June. I am the third owner and it has just over 10k miles. I am using an unaltered 2230BD00 map. I tried the same map with the O2 sensor off, but I could not get it to stop popping on decel, and the CO trim was as high as 14. The sync fixed the vibes and the power is more linear from 3k up and it still can rev. I try to keep it above that rpm so it doesn't lug.