persistent and odd fuel ration

Carbs are rebuilt and clean. Coils are brand-new Dynatek, points replaced with electronic ignition. Plug wires are new. Choke plungers rebuilt. New fuel lines, new spark plugs, and a Pingel dual-outlet petcock.I am not trying to turn carbs into fuel injection.At idle, the bike audibly stumbles, and that stumble happens at the same moment the AFR spikes. I don’t know which is the cause and which is the effect.Cylinder #2 shows intermittent pockets of lean AFR. Cylinder #1 does the same thing, but to a lesser degree. These traces are all at idle (~1000 RPM). The issue largely goes away if I raise idle speed to ~1200 RPM.The bike is fully warmed up, but the issue is worse when cold. I don’t believe there are intake or exhaust leaks. Carbs have been synchronized.For reference on the graph:
• Green ≈ 12 AFR
• Red = anything above 14.7 AFRThis puzzle probably has nothing to do with jetting, and I’d prefer not to go down that rabbit hole—but for completeness, here is how it’s currently set up.Dec 20 update (after rebuilding choke plungers):
Everything seems to go lean on throttle snap.

• Cylinder 1:
  (Pilot 10 / Main 100 / Clip 2 / 3 mm)
  Small AFR pops at the same frequency as #2, but much smaller. Otherwise AFR looks good.
• Cylinder 2:
  (Pilot 12.5 / Main 102.5 / Clip 3 / 3 mm)
  Large AFR swings—almost like a backfire, but still within range.
• Cylinder 3:
  (Pilot 10 / Main 105 / Clip 4 / 3 mm)
  Perfect idle.
• Cylinder 4:
  (Pilot 10 / Main 105 / Clip 4 / 3 mm)
  Idle is too rich; pilot screw is almost fully closed.

Looking for insight specifically on the intermittent lean pockets at idle and the synchronized stumble—not general jetting advice.
 

 

This effect (at idle) can be a result of weak spark. Have you verified that the supply voltage to each coil is stable, and within 0.5V of the battery voltage (12.5V to 13.8V).
Higher (than normal) resistance wiring ( ground and power) to/from coil terminals, CDI and voltage regulator will be the culprit, or, possibly a failing battery or charging system.
Also, verify plug gaps are correct (0.6 to 0.7mm)
 

If I am reading it right it's no surprise performance is bad, your jetting is not consistent 

This is good. it makes sense enough to follow up on. All the wiring to the coils is new. I did replace the rectifier and regulator with an all in one for lithium. lithium is at a lower voltage and i havent confirmed everything. This is a good direction. thank you

Enough people have told me that they should all be set the same way that there is something to what you are thinking. I just cant help think the jets are the cause and the effect is the AFR.  The afr is where it should be so by that logic the jets are where they need to be in order to get that afr. the AFR is correct and then pop, its off for a second and then comes right back.

Lithium batteries are a no for this application the technology is not compatible with the charging rates, the jets should all be the same.
I recommend you get someone that knows what they are doing to help you with this.

Why would the spark problem only appear on two cylinders that arent on the same coil/circuit? the coils and ignition module are Dynatek and the voltage is within the specifications running or not running. The voltage regulator is made for lithium. What specifically are you saying?

If all the jets were the same there would be cylinders that wouldnt run. There are no leaks, the jets are smaller than expected. I’ll probably take the filters and exhaust off to see if they are slowing air flow. Idle jets are at 10. I dont think i can go smaller.

As my previous suggestion.

Given that AFR is "computed" after  combustion, you can/will run around endlessly... until all the "primary" requirements are met. 
You mentioned "filters"... are "pod" filters fitted to individual carbs?
These, especially Chinese cheapies are notorious for causing bad running, as their locating flange obstructs airflow into the pilot circuit as well as the passage that leads to the top of the diaphragm.
 

Yea, when I get a chance I’m going to take the filters off and pull the exhaust off.