Speedmaster running on 1 cylinder

The simple version is this:

I have a Speedmaster 865 2005 with only 4k on the clock that has been off the road for 18 months due to illness. I went to start it and it ran but really badly, drained all the tank and gave it fresh fuel but no difference. My local bike shop said carbs needed rebuilding and this was done but 10 miles later the problem is back. They then said the pick up sensor was also gone and they did this as well, 10 miles down the road and it was running really awful again. Over £300 later and I had lost confidence in that particular bike shop.

I called an old friend who is a car mechanic for Ford with over 20 years on the tools and he immediately said it is only running on 1, sure enough you pull off the nearside HT lead and it makes no difference. Now here is where we need some advice. He took the coil pack, the HT lead and the spark plug and swapped them over expecting it will either be the same or most likely it will swap the fault over, the result is that it doesn't run on either POT!

He says there are 3 explanations for this and I need to get advice as he is a good mechanic but has no technical knowledge of these bikes. The options are:

1) The coil packs are coded and swapping them mean that the coding is wrong and neither fire. He is sceptical that this is the case but he said to ask before we waste more time on it.

2) We have a dead coil pack on the nearside POT and swapping it over to the offside only mean that that side won't run either. The fact that the nearside still doesn't run with a good coil must mean there is another fault. Does anyone know the resistance reading for these coils?

3) If it is a dead coil pack and a 2nd fault on the nearside POT then me thinks the fault could well be with the pick up sensor. He made a few calls and he seems to think that if the air gap was set wrong then it is possible to only fire one POT but he doesn't know enough about the pickup sensor/ignition.

I am confident I have a very good mechanic but we lack a little technical knowledge on this bike. Any advice would be very much appreciated.