Placing a load on the battery reduces the voltage. Loading it more reduces the voltage more. Your switch bypass allows the haeadlight load to add to the starter load and drag the voltage lower than what was necessary.
The voltage output potential of the coils is proportional to the voltage it receives from the battery.
If the spark gap is increased, more voltage is required for spark. Could be you have some spark plug boots where the resistors have opened to cause an additional gap. Then the low voltage due to headlight (I can also imagine and brighter, higher wattage headlight installed) and the load from the starter motor, dip the voltage during start to a level below what is needed to bridge all the gaps in the coil output circuit.
There are some other possibilities.
The condenser for the 1-4 may be leaky, and this effects the voltage input to the coils and how briskly they can fire the spark plugs.
Further, point contact deterioration may be adding resistance to the 1-4 primary circuit, which in turn, effects how much spark voltage can be developed by the coil for the existing spark gap.
Lastly, when was the last routine 3000 mile tuneup done to the bike?
Cheers,