What brand air filter ?
Brand of muffler ?  baffle ? straight through or other ?
What jets do you have in now ?
Other than filter & muffler, everything else stock ?
Was it running fine before the filter/muffler ?

And the cone filter is k&n cone

Do you have jets already ?
What lis the model year ?

You'd only be a little lean from an aftermarket muffler but a cone filter makes it real real lean

It depends a bit on the elevation you ride at......with the stock air cleaner and a DYNA or stock muffler, a #150 main, and a #50 or 52.5 pilot works well....with 3 number 4 machine screw washers on the needle in place of the stock white spacer.  (If you still have a lean surge at low throttle settings, remove 1 of the washers and try just 2).  Higher elevations require smaller jets.....but until you get up over 4,000 feet I am not sure you need to change much.

With the cone filter folks tend to need a bit larger jets....I would start with a #152.5 main, #52.5 pilot, and 2 washers (unless you are over 4,000 feet msl).  Each bike is different.....but obviously you are running lean with what you have right now.

Black smoke is definitely overly rich......which means you likely have a problem other than just jetting.

What petcock do you have?  Did you check the float level when you had the carb apart?  Does the choke lever work properly (spring loaded and notches into position....and stays close)?

Generally the float level adjustment is not so critical that it will cause what you are experiencing - however if the float is installed upside down (happened to one member), or the float is damaged or has a hole in it, or the needle and seat are defective and allowing too much fuel in the float bowl.

Or......there is the possibility that like one forum member your pilot or main jet has come loose and fallen into the float bowl....or you left the brass washer off the main jet and the needle jet is moving around.

I think the carb needs to be looked at.