The inner and outer cylinders are on coil boundaries. Have you looked a spark quality differences inner to outer cylinders. If you swap condensers on the points, do the symptoms follow the condensers? What about carb vacuum sync? Are the pods oiled... equally? Is the timing correct for both point sets? Have you checked the carb coupler boots for leakage?
The slide needles dominate at a different throttle position than the mains. So, a general spark deposit condition would average these two contributors and be highly sensitive to the time spent at each setting. Standard isolation technique is a "plug chop", where you see the deposits left after operation at a single throttle position. (slides are direct coupled to the twist grip, RPM is reactive.) Have you put in clean plugs and done a WOT plug chop?
As far as plug color the outer two are a dark brown and the inner two are tan. .... The outer air screws are one turn out and the inner two are a 1/2 turn out.
The pilot adjust screws don't contribute much at mid and WOT. They are mostly and idle balance.
Are there any bike alterations that could effect the air pressure/volume that reaches each carb throat entrance or bowl vent?
Are your jets drilled or as they come from the factory? Are they Honda manufactured?
Can we be assured the carbs are clean and all the air jet passageways and emulsion tubes are free to flow fully?
