Be aware, I am just trying to help you, not just run you around in circles. But, the endeavor is difficult without any hard data to analyze.
Latest - rejetted carbs to a #100 main jet (stock is 98),
Probably still too small a main. The #98 was selected because of the stock high pressure muffler. All the 4 into 4 used a #100 main.
I really think you need a WOT plug chop to zero in on the correct main jet size. Multi throttle position ride arounds aren't going to get you the proper information to make a predictive change, imo.
Am I correct that you have changed the venturi shape on these carbs? If so, that is a serious change in pressure drop when the air velocity increases. Probably much less than before, which would seriously change the flow rate of any fuel jet installed. Further, if the shape is no longer round, then I suspect there is also atomization issues, too.
left slow jet at #38 (stock) and needle at 2nd clip down from top (stock).
This needle position only applied to the stock CB550F engine/muffler with the paper air filter.
The K models with the exact same engine, filter, and only the 4 to 4 exhaust system change, had the needle in 4th position from the top. So, the question is, do you think your current set up is more like the 4 into 4 tuning or the F model high pressure single muffler?
Retained the Unipod filters and set air screws at 1.5 turns (stock). It still burbles and hesitates at low throttle openings and immediately off idle.
I'm thinking your description of burble is different from mine.
Anyway the 77 Cb550 F had the stock pilot screw sett as 1 1/4 turns. However, with the shortened intake tract and pods that is almost certainly to lean for an acceptable throttle response off idle. It's going to be less 3/4 to 1 turn max, when using the #38 pilot. The pods may even demand a #40 pilot jet.
I'll make this point again. I simply don't believe you can compare the PD carb jetting to the early style carbs (022a,069a, etc.) It is very easy to see the venturi shape has changed between those carbs. And, I suspect that one of the improvements associated with those PD carbs is improved atomization, as Honda and Keihin were working toward the EPA 1978 mandates.
Notice there is no 1978 CB550F? The product line for the F ended in 1977. Only the 78 CB550K with the PD carbs made the grade.
If the venturi shape has indeed been altered, who knows how well these carbs can work at any but WOT.
My advise is to find some PD50 carbs from a CB650. You can run the engine lean at idle and the accelerator pumps makes throttle twist a joy. You'll still have to tweak jetting for best mixtures, as no engine has the same demands as what you have configured now.
Cheers,