engine skipping?

[bdgt250x]

Hey, Ive been noticing that when i rev up my engine sounds almost like its not firing every time, its like thump..thump..thump..thump...........thump..thump. .thump..thump.. and its also making my plugs black.
Ive just rebuilt my valve train, put on new valve seals and i bored my engine a couple of months ago and put in new piston and rings. my carb seems adjusted right, it doesnt seem rich or lean so im wondering if some of the 15 year old electronics may be messing up. i guessed it could be either the cdi or ignition coil and my manual says it could also be the pusle generator or the alternator.
i was just wanting to see if any one here had any ideas of what it might be before i started spending money again!

Thanks

[honda300EXtreme]

to me it definatly seems electrical,, and since you have a manual you will basically have to test the cdi, coil and alternator, and eliminate it one, one by one,,



but then on the otherhand you say you plug looks black, so that means you running rich so the "skipping" your feeling could possible be a rich Bog,

[Caseys 300ex]

Adjust the air fuel mixture at the bottom of your carb. Its under u carb and its a little screw that takes a flat head. Mine did the same thing and that was the problem