I fail to see how syncing would improve this situation.
Fact... I had totally disassembled the carbs months ago to rebuild them.
When you rebuilt the carbs, did you replace the old, hard orings? Particularly the ones on each main jet? Leakage here can upset fuel metering over the entire throttle setting range.
Because of the four individual carbs, the cylinders try to behave as four individual engines. The carb slide position would determine the firing speed of each cylinder if they weren't linked together with a common crankshaft.
Let's say number 2 had a slide position of 900 RPM and the rest had a slide position of 1100 RPM. The resultant actual RPM might be 1050 RPM, with #2 hardly contributing and getting a lean mixture for that RPM. A slight backfire through the carbs could result from a lean mixture.
During cold warm up, do the head pipe temps come up evenly? If not, which ones take longer?
Can you equate the presense of the PFT with choke operation? And, are you certain that each choke butterfly is in an equivalent position with the others over the entire application range?
What is your air bleed setting? Are these the same across the bank? Float levels? Slide needles: size, shape, and position?
I think if you want all four cylinders to behave the same, you have to be certain all four carbs are behaving the same.
Cheers,