I've not read this thread thoroughly, but I had a similar 'ish' problem on my own bike many years ago. After a catastrophic RTA, which left my bike and the car that pulled out in front of me, as burnt out wrecks, I salvaged what I could and eventually rebuilt it. After all being fine for several months, it started getting an occasional misfire and this got worse and worse. It bugged me for several weeks, but I could not track down the problem. Eventually it died completely (on the way back from Norvil as it happens) and I had to be rescued by the RAC (roadside recovery for those who don't know). The rescue guy was a motorcycle specialist and he was determined to track down the fault (our bikes a very simple after all!!!). He persisted for a couple of hours, but eventually had to admit defeat and we loaded her into the back of his van.
After getting back home and kicking the dog, I tried kicking the bike and, of course, it started first kick. The bike was in the garage, it was getting dark outside and I had not put the garage light on. In the gloom, I thought I saw a spark from around the oil tank area and sure enough, there was the problem. Due to some inexpert wire routing when I fitted the new harness, a power lead was rubbing on the frame. Over weeks and months, the coating on both frame and cable had worn down to the metal.
Different factors, such as engine revs, gear selection, road surface and angles of lean, determined whether or not the cable was in a position to short out or not. This point of shorting was very difficult to see without knowing where to look and, of course, I went through a whole manual of possible reasons for the misfire before having the good fortune to start the bike in near darkness.
Sorry if this possibility has already been discounted, but the information may help someone else. Otherwise, I can only offer my sympathy as I know how totally pissed off you must be feeling right now.
Bob