The symptoms are also similar to the coil/s being faulty.
I know that you say that you have new coils fitted, but if you are still in possession of the old coils, if they were servicable, you could substitute them? This would eliminate the coils....or not, but it is best to do one thing at a time in my experience.
Check that youre air vent in the petrol tank is clear. When the symptoms start, you could release the filler cap and see if there appears to be a vacuum.
A problem that I had on mine when I was first running it after building was at 3500 to 4000 revs whilst cruising in top gear, or accelerating, it would missfire and hesitate and I was confident that it was an electrical problem such as bad H.T. lead, but the cure was to drop the needles down one notch to weaken the mixture, much to my suprise (and I have dropped them another notch also and it runs fine now). This was running with early type air filter, peashooters 260 main jets and 3.5 slide if my memory serves me correctly.
Your main jet doesn't sound too big, but what size air slide are you using, and do you have black caps or peashooters on?