Paul,
This sounds as if it started as a carburettor problem (an inbalance between the 2 carbs). It could be down to throttle cables not adjusted correctly - so that one cylinder pulls harder than the other, or possibly dirt in the bottom of a float chamber. The float chambers have a guide hole in the bottom for the float needle - they some times get partially blocked by dirt, thus restricting the movement of the float, thus ending up starving that cylinder of fuel.
Please do NOT repeat your test of which cylinder is firing by removing a plug lead - this is the easiest way of ruining a Lucas magneto, as the spark will have no option but to short across the windings. (BTH magnetos had special spark gap screws to prevent this happening!).
I would suggest you check out both float chambers, then set both slow running screws to 2 turns open, and the throttle stops so that they are just lifting the slides, and there is some slack on the throttle cables. Start the engine and get it running smoothly on both cylinders and down to a steady tickover. Finally, adjust the 2 throttle cables so that both cylinders pick up together.
Also, engines that have the carbs out of balance often suffer from smoke from the cylinder that is running lazy, as that cylinder tends to draw oil past the rings.
Regards,
Eddie.