Thanks TT... So just to clarify... you suggest to rebuild the carbs to 550K specs vs. 550F? So stay with the #100 mains and #D26 needle of the 550K? Needle clip positions the same as well? Is that because the UNI nu-4055 will potentially lean things out? And the less restrictive exhaust also leans things out? Am not doubting your advice in any way, just want to understand why for my own learning. 
I don't recognize the #D26 needle nomenclature as being a Honda number. The needles from Honda were 272304. I don't know if the needle profile is the same between these two numbers.
Jet needle number 272304
Jet needle OAL 5.57cm
Jet needle diameter at tip 1.25mm
Jet needle diameter at 1mm 1.63mm
Jet needle diameter at 2mm 2.06mm
Jet needle diameter at 3mm 2.49mm
Jet needle diameter at 4mm 2.52mm
Jet needle diameter at 5mm 2.55mm
Others have discussed tuning issues with some after-market needles in these Hondas, and have gone back to stock for corrective measures. Let us know what works out for you , OK?
All the 550 motors used the same mechanical specs for the engine proper, regardless of year or model. The only thing that changed was carbs and pipes. The F model pipe apparently worked so well that the fuel draw at WOT needed to be restricted at #98. Other 4into4 models with the same style carbs got #100. You don't have that nice pipe anymore, so go up to #100 at least. You may find out eventually that an even larger main is required, particularly if you aren't done with exhaust and induction changes.
FYI, I have a couple of F model 550s with the stock pipe and also use the Uni filter along with the 069a carb in stock configuration. The set up works well for me.
In theory, the Uni filter lowers the carb throat vacuum, which pull less on the existing jet orifices and changes the fuel mix slightly.
A good 4 into 1 race pipe system will help scavenge the cylinders at high, near red line or above, RPM. This allows more oxygen to be available for the next cycle, and therefore the need for more fuel to pair off. The trade off, is that below those lofty RPM figures, the exhaust pulses are reflected back to other cylinders, and foul their ideal scavenging. Honda made their pipe a little more restrictive over the entire RPM band, in order to improve overall responsiveness in the RPM band most used on the street. Since the cylinders don't have as much air replacement at screech RPM, they require less fuel delivery for those throttle positions/speeds.
Of course, operating at screech RPM reduces the overall life of the pistons/rings/cylinders. But, racing enthusiasts frequently sacrifice longevity for immediate gains/thrills.
Cheers,