Are you sure the electrical system is right? Timing, good spark, newer plugs correctly gapped, etc?
Are the valve clearances reasonably correct. This has a big effect on the carb synch and therefore the mixtures.
Are the carbs for SURE clean and are the various o-rings inside them in good condition? You replaced the manifold o-rings, correct?
You have a 5/16" fuel line, the vacuum nipple is capped at carb #3, the gas cap venting is clear, and the two floatbowl vent lines are removed and the vent nipples are open?
You retained the two jet needle plastic spacers, the thicker one ABOVE the e-clip, and the thinner one BELOW the e-clip, when swapping to the DJ needles, correct? (The DJ jetting spacer always goes on top the e-clip, if needed.)
Have you correctly re-adjusted the floats close to .94/95"? Did you check both sides of each float to be sure they're not tweaked?
Are the pilot screws (underneath) about 1 1/4 to 1 1/2 turns out? Are the side air screws set for highest rpm?
You said the vacuum synch went well. So the levels are very close to each other. At what rpm did you set them at?
All jets are tightened firmly?
The exhaust header gaskets are in good shape?
Jetting can be difficult, so I have to ask you all this stuff so I can get an idea. ALL THE ABOVE is important. Any short cuts to cleaning, adjusting, not replacing worn parts, etc, will just cause frustration and a waste of time. Let me know what's been done and I'll tell you how to test and get your bike running right.
I would possibly try your e-clips in the 4th position from the top WITH the jetting spacer on top the e-clip. This means a new vacuum synch must be done. But FIRST answer my questions and tell me again how it's running.
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