NC30 Ignition problems....

Me mates NC30 was thrown together a few months ago to try and build her up for this trip to Le Mans. When we put her back together there were certain things we did along the way that were gonna be properly sorted later. For example, we opened up the carbs, cleaned and air blew them out, and when putting the pilot jets back in we screwed them all the way in and reassembled them onto the bike (thinking we were gonna get them tuned properly later). Anyway, even in her 'lean' state (pilot jets all the way in) she has been running and starting reasonably well, with obvious flaws in low down pick up (once she's on the main jet no problem). 

We took her out for a final shakedown before the MOT and we noticed a tapping sound coming from the engine at idle. Thought Id mention it to the MOT garage, they suggested after MOTing it, that the right rear cylinder (no. 3) was misfiring due to. Perhaps due to running lean? - we guessed. (seeing as we knew we'd turned the pilot jets all the way in). 

So took her home, carbs off, pilot jets out from bottom by 2.25 turns, put them back on and she ran but still with the misfire. We were looking for air leaks as the carb/cylinder head rubber tubes are a bastard to get on properly, when me mate noticed that the wires goin to the coil packs could have been the wrong way round? we checked the Haynes and apparently they were.... and as were the front pack??? However, due to how the coil pack works, the engine would have never run with them the wrong way round??? so we swopped them for what looks like the correct way round  (Haynes wiring diagram), and it wouldn't start, so we swopped them back to apparently the wrong way round but was how it was working before and now it wont work in that way either! 

Very frustrating, especially when you've got a 2000 mile euro trip planned for the end of the week!