You definitely could have electrical issues.  It can cause your bike to sputter.  Check for bad grounds.   I also suggest putting a volt meter on your pickup (also make sure it and your flywheel are both clean and rust free)  Test your coil and cdi.  There is a downloadable manual on this site that has all the resistances.  What spark plug are you using?  Check your plug wire and boot and make sure there isnt corrosion where the boot connects to the wire and at plug.  Is the boot stock?

Here is how the circuits in your carb work.  Keep below in mind when jetting and only adjust 1 circuit at a time:

idle - 1/4 throttle = pilot

1/4 - 3/4  =  Needle   --  (Raising the needle = Rich)   ( Lowering the needle = Lean)

3/4 - full  =  Main