That range you're having problems (2k-6k) is largely controlled by the pilot screws, I'd look through some of the other tuning DIYs (
this one by Vex is the main one for pilot jets here, and
this is the one for shimming the carb needles, by Kkim). Frankly I'm too braindead from work to make a suggestion about which way you want to adjust the pilot screws, but I *think* you may want to push them in a smidge, as raising the needles has introduced a lot more gas in the midrange, possibly richening the mix overmuch. Definitely take a look through the tuning DIYs, or go to thedark side & read thru the
intake FAQs @ ninja250.org
Regarding the washers; the needle, washers, and retainer all move together as the boot moves up and down with the diaphragm. Doesn't matter overmuch that the washers were a bit too snug in the retainer, so long as the retainer fit snugly on the needle top to keep it from coming up on its own (the spring & retainer are there to keep it seated in the plastic part of the diaphragm slide (hard plastic part).