Just to be clear, you are
raising the needle by
lowering the needle clip. The lower you move the clip the higher the needle is raised. By adding pods and, what I assume is, a freer flowing exhaust you have leaned out the overall a/f ratio. Jumping up to 110 mains only addresses about 3/4 - WOT. The needle clip affects more of the mid range of throttle position. You can test this by slightly closing the choke when you feel the bike stuttering and losing power. Adding some choke will richen the mixture and hopefully will smooth out that throttle position.
I wasn’t joking about putting the air box back on. Honda’s engineers did a lot of work to make the bike run well. Making drastic changes means you will have to redo this carburetor tuning work which most people don’t know how to do or don’t have the patience for.
The best thing you can do is find a dyno that can tune old bikes. I brought my CB674 hybrid up to Rick Stetson at Harry’s Machined Parts in Northborough Mass. The guy knows his stuff.
Maybe this picture will help.