Those are the first thing I checked. I basically ripped out a perfectly good ignition and coils.

 

What the heck makes the rear cyl exhaust go fluff, fluff, fluff, fluff after reving the engine, but does not do it cold.???????

 

Is it starving at idle or a carb problem? wouldn't think so if only one cylinder fluffs.

 

It's hard to say. I have a CV instead of a S&S, but mine idles lower until warmed up. Once warmed up the idle smooths out and increases.

 

Did you try backing the idle mixture screw out a little, like 1/8th to 1/4 turn? Any change?

 

Yes I tinkered with the carb adjustments and went back to the original
42 main jet today. Bike runs like a rocket over 2k rpm.
Carb problems would not make only 1 cyl miss.?

 

Is it only missing at idle? Maybe posting a video would help out.

 

Making a video & posting it on youtube is a pain.
Yep misses at idle and smoothes out about 1500 or so.

 

Just cranked it up cold and ran great even without choke. after it warmed up ideled like crap again??????????? WTH

 

Does the exhaust pop on decel? Does the carb spit or backfire? Just making sure you eliminated an exhaust leak.

I know you checked for an intake leak with carb cleaner, but what you describe sounds like an intake manifold leak. I would check, or maybe just replace gaskets, and check condition of manifold. Good luck.