Hey again,
Okay, first off, the sharing tunnel would be ABOVE the pilot jet looking at the carbs upside down...and in that photo, I don't see one...so you've eliminated that as a problem...so no caps on the pilot jet towers.
Next, the long brass tube on the edge of the carb body in the lower right corner of your photo is the enrichener tube...it's NOT the jet...the JET is in the float BOWL. But anyways....carb cleaner or fuel should flow thru that brass tube upwards and into the enrichener chamber....you should unscrew the enrichener plunger and remove it so you can better access that pathway. Sounds like you need to get some fine wire and start probing and spritzing with carb cleaner up into that brass enrichener tube to get it open and flowing. Also ensure that the JET in the float bowl is open and free flowing as well. THEN you should be able to start the bike with the enrichner.
As for the 3500 rpm...you said you turned the pilot screw all the way OUT!
OUT or CCW is increasing/richening the Air/Fuel ration providing more air/fuel. Turning it IN or CW is reducing/leaning the A/F ratio supply. I didn't reread this whole thread so I can't recall if you have Genuine Mikuni jets..mains and pilots vs. Generic...can't see the top of the main jet very clearly to see if it has the Mikuni superimposed diamonds/squares on it?
Bench synching the carbs using the opening/exposure of one of the 3 small ports in the upper carb throat that the butterfly will partially close/cover.... can provide a more accurate bench synch than the breadstick tie method!
T.C.
Okay, first off, the sharing tunnel would be ABOVE the pilot jet looking at the carbs upside down...and in that photo, I don't see one...so you've eliminated that as a problem...so no caps on the pilot jet towers.
Next, the long brass tube on the edge of the carb body in the lower right corner of your photo is the enrichener tube...it's NOT the jet...the JET is in the float BOWL. But anyways....carb cleaner or fuel should flow thru that brass tube upwards and into the enrichener chamber....you should unscrew the enrichener plunger and remove it so you can better access that pathway. Sounds like you need to get some fine wire and start probing and spritzing with carb cleaner up into that brass enrichener tube to get it open and flowing. Also ensure that the JET in the float bowl is open and free flowing as well. THEN you should be able to start the bike with the enrichner.
As for the 3500 rpm...you said you turned the pilot screw all the way OUT!
OUT or CCW is increasing/richening the Air/Fuel ration providing more air/fuel. Turning it IN or CW is reducing/leaning the A/F ratio supply. I didn't reread this whole thread so I can't recall if you have Genuine Mikuni jets..mains and pilots vs. Generic...can't see the top of the main jet very clearly to see if it has the Mikuni superimposed diamonds/squares on it?
Bench synching the carbs using the opening/exposure of one of the 3 small ports in the upper carb throat that the butterfly will partially close/cover.... can provide a more accurate bench synch than the breadstick tie method!
T.C.
. Finially, remove the dern carb bank, disasemble each ccrb incncluding ALL jets and floats. Spray QUALITY carb cleaner thru ALL ports to make sure they are open,including enricher circuit with plunger pulling enricher shaft outward. Use a pointy tooth pic(no metal) and run in those pilot jet sideholes


)
Like you and CM400 said, the little holes are in all different positions around the tube, not necessarily pointing in one particular direction, since it just needs to get air from that channel at the float bowl. 
. I DO know ome thing at a time van save alot of tail chasing, /hope he's got lots of bunnies to turn looose down the perverbale 'rabbit hole'..............this gonna go on for a bit
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