Let me be clear on one thing before we get into this: the stage 1 Dynojet kit that I've fitted to my Honda is great. Combined with the new exhaust headers, the result is awesome!
Simply put, there is now more of everything, everywhere in the rev range. More power, more torque, more acceleration, more top speed, and all of it is smoother and more tractable than before.
Now, here's what came with my kit: a selection of main jets, let's call them small, medium, and large for the sake of argument. The small one is for high-altitude applications, very cool but we're not riding up the Andes so... nevermind. The medium one is for use with stock (i.e. restricted) exhaust headers. The large jet is the one I used, and is for the larger, unrestricted exhaust headers.
Then came an adjustable needle, with an E-clip and plain washer for fitment, and instructions for how to set the air/fuel idle mixture screw.
I'll explain what happened and how I corrected the problem, this is probably tedious reading but it could be useful to anyone out there fitting the kit to their bike.
When I reset the pilot mixture screw, and replaced the needle, I noticed two things.
First, the screw was set at more than four (!) turns from seated, whereas the factory setting is about two turns. That is a massive difference, and not even the Dynojet kit is set to be that rich.
Second, there was a small rubber O-ring under the needle.
Initially I didn't give these details too much attention, I just set the screw at three turns as specified by the instructions, and replaced the needle including the O-ring, since the instructions say to include all stock spacers. Then, when I noticed that the engine was running worse than before in some respects, I started to put the pieces together. The mixture screw set so far out (i.e. rich mixture) and the needle raised by that O-ring (again, rich mixture) must have been an attempt by someone in the past to richen the mixture, which on these bikes is very lean as standard, to comply with emissions regulations. Since the standard needle is not adjustable, the only way to raise it (thus richening the mixture) is to put a spacer underneath the head. Crude, but effective.
So, I took the carburetter slide out again, and took a few measurements to compare the stock needle with the Dynojet one. Long story short, the little O-ring (see photo below), which I had kept with the Dynojet kit, thinking it might have been a stock spacer, was in fact raising the needle by just over 2mm... that's huge! No wonder it was running like crap and the fuel consumption was through the roof!
With the O-ring removed, and the needle set as intended, throttle response is, in a word, crisp.
There are no signs of hesitation or flat spots anywhere to be found, it just responds instantly, ready to go.
Incidentally, there is an interesting write-up on carb cleaning at this link, with some excellent detail photos. You know, since I didn't take any photos while I was doing mine...