I should also state that this only happens during the initial start of the day, pulling the choke starts my bike up just fine, but if I did that every day I started her up I'd loose an easy 15 mile range, perhaps one can hone in on this, that was the pattern I noticed, so I just don't bother pulling it. I also had the same characteristics with my super hawk. Now with the newer parallel twins and perhaps I4's, 05 & up, you shouldn't have that "problem" with start up. I didn't in all the years I had my 650r 45k mi on her too. My dads 750ninja was a different story....
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2001 rc51 upgraded
1999 vtr 1000 "superhawk" sold
2006 650R Ninja sold