I have just had a similar problem..

I reckon its fuel.

I changed over my coils,cdi's,rectifier etc and nowt changed...

Took of the carbs,thoroughly cleaned the jets,air screws,air holes etc and now its fine..

What I assumed was happening was..

When you start the bike its had time for the fuel to go down into the float chamber,when you run the bike it runs on the fuel in the chamber,chamber empties plus a little extra fuel thats trickled down,but theres not enough flow to keep bike going ?

my carbs looked immaculate before I cleaned them too...! , I cleaned the little holes with a strand of hair like thickness speaker wire.

Its a piece of cake whipping out the carbs and doing this,it wont do any harm to do it anyway.

hope you get it sorted .