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If it runs like this for the rest of it`s long life i`d be fine with it, if the bike was carbed , but having F.i. it should run floorless.
You're putting WAY too much faith in F.I. The biggest problem with bikes, carbed or F.I.'d, is the "zero flywheel effect."
There's just not enough inertia in the spinning bits of a motor with no flywheel to keep the motor spinning smoothly when a cold-engine misfire occurs. That's why an 1100rpm idle has been suggested over and over and over again on the forum. Keep the revs up 'til the motor warms up and ignore the occasional fart/bump/clunk right after a cold start.
Why does my wore-out, 15 year old Honda Civic idle so smoothly at 600rpm when cold, when my state-of-the-art motorcycle farts and clunks occasionally until the temp is up to normal? Easy-peasy....the Civic has a 45 pound flywheel smoothing out the rotation of the motor. The FJR has **** for inertial assistance.
And on a final note, I'll put up a set of Keihin FCR flat-slide carbs up against any F.I. system any day of the week for overall smoothness and performance gain, if you can stand the rattle those carbs produce, and don't mind dicking with them constantly. LOVED they way they transformed my ZRX. HATED the way they sounded like an old Mercedes 240 diesel with all the slide clatter.