Thanks TwoTired - would the small displacement and weaker draw account for the leanness?
Didn't I just say that?
The 500's smaller displacement doesn't suck as hard on the carbs, making less vacuum in the carb throats, and therefore less draw on fuel metering devices.
Pardon the confusion, but I'm certainly no expert in these things. Moving the needle clip to the lowest position has certainly improved the bogging and popping.
My assumption is that to make the 500 run as well as Honda tuned for that displacement, the recipe for tuning to that displacement is the same as the CB500K3.
You should make sure the float height is 14.5 mm. You have to use the same air jet, #120 instead of your current #130, and you would also use the slide needles for the 500 configuration which are E2350F clipped in the 2nd groove, instead of the CB550 slide needles which are E2349F clipped in the 3rd groove. Do that, and it should run perfect, right out of the box, like it did for Honda off the showroom floor for the CB500K3.
You'll probably have to get the needles, maybe the air jets, from a European source. Maybe BryanJ can help you with part numbers. Or, get creative about modifying what you have. I don't know how to decode the Honda needle numbers to determine their taper angle, overall length, and starting diameter.
Otherwise, keep futzing with your current carb adjustments and trying different parts, until you are happy with how it runs. But, essentially you have the same problem that others have when they change to pods or a different exhaust system, where a dyno is the fastest way to the dial in the proper carb settings.
Maybe putting another groove in your needles, or shimming them to raise them even more will help your run issues. I wouldn't change the main jet size unless a WOT plug chop said it was necessary. And, I note that Honda thought a bigger main jet WAS unnecessary. They solved the midrange issues with a different slide needle taper and position, along with the smaller air jet. The smaller air jet also richened up the WOT throttle position, too, I expect.
You did resynchronize the carbs after changing the needle position right?