It may just be that the jets either need cleaning or replacement. I had chased a fuel delivery roast for months only to find myself right back at the same jetting I was before the problem started and everything seems to be at 98% better. Still have a slight hiccup, but over all, the bikes running much better.
Jets are cheap and easy to replace. While you have the pilot jets out, you may want to pull the air mixture screws, being careful not to lose the small spring, washer or rubber 'O' ring (but first, screw the mixture screws in and count how many turns it takes before they come to a dead stop[This will be the number of turns you set the screws to when you replace them]). With the air mixture screws out, blow carb cleaner up into the carb bodies until the carb cleaner comes out the other hole (i.e. shoot cleaner into the air mixture hole until the carb cleaner is coming out the pilot jet hole and vise versa), then before the carb cleaner has a chance to evaporate, hit it with compressed air trying to blow out any possible obstruction. Then make sure when everything goes back together, the air mixture screws are set at where they were before they came out.
2014 Scrambler: Arrow 2-1 high pipe. TTP Tune 4 with Breathe airbox cover no baffle.
Past rides:2008 T100, 1975 Honda CB400/4, 1989 Honda GB500, 1965 Honda CB450 Black Bomber, 1972 BSA A75 Rocket3