The capacitor holds very little charge. Less than what it takes to charge the ignition coil.
The ignition coil pulls about 4 amps when it is charging. Its not a constant draw. On a points bike the duty cycle is about 50%, meaning that the coil is charging half the time. I'm not sure what the duty cycle of the Boyer is at kicking speed but imagine it would be less than 50%.
At kicking speeds, the output of the alternator is low. Not enough to deliver 4 amps to the ignition when it needs it. When the alternator is not charging the coil it can charge the capacitor. The capacitor alone can not store enough power to charge the coil. When the ignition needs power it can draw it from both the alternator and capacitor. Which will drain the capacitor.
It would seem that simply using a larger capacitor would fix everything, but that only works to a point. Remember that the alternator output is low at kicking speeds so it won't be able to charge a super huge capacitor in the short time between ignition dwell.
Your best bet for a batteryless system is energy conservation. If you haven't already done it then wire up a Start Mode switch that will disconnect everything but the ignition when starting. Eliminate everything that is not absolutely necessary and replace bulbs with LEDs. These last two won't help with starting, since you switch them off, but it could prevent the bike from dying when you switch everything back on.
A more efficient ignition will do wonders. With my HEI ignition, I don't even have to turn off the headlight when starting. It only has about 8% duty at low speeds so it can get most of it's charge from a small capacitor. The capacitor charges for 92% of the time so it is guaranteed a full charge, even with the lights on.
