Forget the plug chops. Those probably won't help you much if you don't tune bikes all the time and know what you are looking for, the pics on the net are only easy to read if you have something drastically wrong with your bike/tuning.
Couple of questions:
Carburetors are clean of all debris correct? Are you SURE?
Move to the next question if yes...
Does it idle? If so, did you synchronize the carbs? If it idles, but you did not synchronize, do NOT continue to the next bit of info, unbalanced carbs can cause all sorts of "symptoms" that are not curable until you sync the dang things!
Your pilot screw adjusts your fuel or air mixture (depending upon each carburetor's design). What are the stock settings for this bike (see table here http://oldmanhonda.com/MC/DataTable.html) So for your idle to be at stock settings that screw should be 3/4 to 1 turn out. You have modified the intake side and might need to bump it up to 1.25/1.5 turns out. That said, this screw will only cause you headaches from 0-1/8 or 1/4 turn on the throttle. So when you are accelerating from a stop, you would have some hesitation until you got to the mid range, and then it would be fine from the midrange to high end.
If I read your post wrong, forgive me, but it seems that if you are at half throttle (mid range) and you are giving it more gas, it hesitates and then seems to come to life at the higher end right? That would tell me it's got too little fuel in the mid range, and you would want to lower the clip on your slide needles. This pulls the slide needle out of the way earlier allowing more fuel into the carb throat at mid/high throttle.
Neat project, most will tell you things that are "wrong" with your bike. Some are just couch engineers, while other comments aren't really negative, it's just that they learned from their own/other's mistakes and are trying to help. As you found out with XB33bsa's comment about your poor tail light
Keep at it.