OK, so the plugs leads did not fix the problem. After an easy start running it up the hill for a kilometer and getting it nice and warm, and the bike gives the sames symptoms, initially it just dies, I can start easily using the choke and then it will pop and fart mainly showing on Nr. 3 but more generally not running right.
So I am now assuming I have a heat related problem. Indeed starting her up again after leaving her for an couple of hours and having done nothing, (i.e. cold) and she does start nicely - so I think I am convinced this is related to something electrical and heat related. Honestly this is starting to sound like the stator (I have some experience with the 350 on these problems...). As I managed to get a cheap one off ebay a couple of months ago, I have one in stock, so on it went!
This time, the problem changed sides clearly making the right hand cylinders pop and fart - I think this is a different problem - I think the stator I bought is not working properly.... Oh well back to the drawing board!
During troubleshooting I also wanted to test my exhaust valves, and this does not appear to be working either. When troubleshooting this, the motor appears to work, but does not turn the valves at all. If you connect 12 V from the battery to the Pink wire, and the negative to the Grey wire, the motor turn clockwise and reversing the polarity makes the motor turn anticlockwise.
The next electrical test involves testing some hall sensors (part of the electrical motor). Connecting the tester to the green and white and turning the pulley by hand, you should find one spot where the circuit is closed (i.e. low resistance). You then do the same test on another pair to get the same result.
This all checked out fine, although the motor still does not turn when commanded by the control box - so it looks like the control box is shafted. I have ordered second hand a motor and control box, so we should be able to fix this.
And I also ordered a new stator from Electrexworld.co.uk, who provide stators and other electrical stuff for bikes. With a bit of luck I am on the right track, and the bike will finally work in 2 weeks time!