Anyways, if I timed it to one side, the other would either be greatly advanced or greatly retarded, depending on which side I chose to use for timing. My normal timing procedure was to use a test lamp to time statically, and then ride to a friend's place to borrow a strobe to dynamically time to the advance mark. By accident this worked well enough every time and the bike ran well enough for the first couple of years, but one day I must have timed to the 'wrong' cylinder (can’t remember which one now) and the opposite cylinder would not fire in any predictable way. I don't know whether the opposite cylinder was now over-advanced or over-retarded, but the effect was very much as you describe. At the time I had just re-bored the cylinders and fitted new pistons and valves and wanted to have the control to run those new rings in properly. It was very frustrating to have one cylinder not firing or 8 / 12 / 16 stroking and popping at idle, but under power when the revs got up the power would suddenly cut in. The carbs proved to be good and there was a good enough spark. I read up a lot of stuff on the web - an article on Duane Ausherman's site provided a useful test - shine the strobe on the cam nose. This is what I saw.
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I made up an indexing disk and used it to check where each side was firing with the test light. I kept rotating the engine and recording the degree reading. The average out-of-sync reading was 31 degrees. This explained why the second image I should have been seeing was not visible - it was way out of the window. I have now fitted an Omega crank-mounted electronic ignition. (beautiful results), but at the time I discovered the out-of-sync condition, my only recourse was to file down part of the offending side of the points cam (lots of trial and error filing and sanding). This worked well enough that I was able to see at least a 'proper' double image in the timing hole and get them to coincide on a good day. I soon got around to replacing the timing chain and that made a good improvement. A crank-mounted ignition system is the ultimate solution. This is a long winded rave but I trust not too stressful to read. Here is the indexing disk - just a bit of paper with a circular array of degree marks glued temporarily to the alternator rotor -
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I have heard that it is possible to straighten a bent cam nose by judicious tapping with a suitable hammer but it requires a deft touch and measuring gadgets. I certainly did not feel competent at the time to try this. I hope this story will be useful, if only to discount one possibility. If you have a strobe handy, have a look and please keep us up to date.