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I had an issue where the acceleration would stutter at about 4,000 rpm occasionally a few years ago. I put in some injector cleaner the next tank and never had it again. Maybe coincidence but just glad it has gone.
Just throwing it out there, but could it be tyre noise.
I had a similar thing after changing tyres and after doing all the checks you have done (except the spacer measurements, that is a new one for me), that is the only thing I could come up with.
It is also reported on other forums as an...