@Motogiro, the bike has the catalytic converter still on. I've tried it in the past without it, but there was no difference, idle is still rough. Plugs are as good as new.
@TownsendsFJR1300, I have also replaced the stock air filter with a bmc. Do you use your stock or an aftermarket on your bike? Could that be the cause?
Could you please elaborate a bit further on the throttle bodies sync, I'm not familiar with this...
PS: A power commander is out of the question for the moment.
I have a the stock air filter in mine. As for the throttle sync, you need a manometer. I purchased a "Carb Tune" manometer as it has no liquids (SS rods) and was about $85.00 US $ delivered to my door in Florida from the UK.
To adjust, you lift the fuel tank.
There is a block on the left side of the bike with 4 adjustment screws. On each side of the bike(still under the tank) you'll find 4 vacuum lines, 2 on each side (one on each side has a white slash mark on it) , their right next to the frame itself.
All lines are plugged from the factory with a black plastic plug.
You remove the vacuum plugs and plug in the manometer.
The #1 cylinder (furthest to the left) is the base cylinder.
You adjust (after being warmed up and a strong fan blowing on the front of the bike to keep temps in check) the other screws to match the vacuum to #1.
Yamaha spec's allows for 10mm variance, I got mine adjusted down to 2 mm. Most dealerships won't get yours adjusted this close and charge more than $85.00 (I paid over $125 at the dealer for my FJR before I bought mine and it was in spec but not that close)..
I rev mine up to 4 k (for a second) and adjust accordingly. This helped me in eliminating 80% of the vibration of an in-line 4. It helps to have a shop manual, but that's it in a nut shell.
This is the unit I purchased:
www.carbtune.com
Its top of the line and paid for itself many times over... Others have made their own, IMHO, I prefer not to gamble sucking fluids into my engine and pay $85.00...
***Note, there is a throttle sync adjustment screw with spring in the middle that SHOULD NOT BE ADJUSTED..