Timing marks
It isn't unusual for Comet marks to be off, but I've never heard of a twin's marks being off. Which doesn't mean it hasn't happened - but mine wasn't one of them if it has.
There's a comparatively easy way to find out, true for all engines I've ever worked on. It has the advantage of sidestepping variations of - and endless arguments concerning - tappet clearance, whether to time on opening, or closing, or...
The valve lift should be equal at TDC +/- 5 degrees, preferably on the early side.
Is that it?
Yup.
This has proved to be true for my Vin Twin, a Manx Norton, a Rudge Ulster, and a Honda 350 K4 racer I once had. The Honda was interesting since it had an HRC camshaft (i.e. a factory race kit part) and I timed it to the usual IO / EC figures. Then I checked. Both valves had equal lift at 3 deg BTDC.
Hoping that I'd just made a discovery of earth-shattering importance, I 'phoned the guy who builds my Manx motor to ask him about it. He was depressingly matter-of-fact. If the valves of a Manx have equal lift between 5 BTDC and TDC, it'll run perfectly. Bugger. There's my Nobel Prize down the tubes.
I actually timed the Ulster to equal lift at TDC in the absence of any other figures, and it flies, pulling perfectly throughout the rev range.
What would save a lot of time, and cost about £45, is to find someone who knows what they are doing, who has a dyno with an exhaust sniffer. If you Google "highland dynos" you can see what can be done. Since this guy is in Cromarty I don't expect to be accused of advertising, but I'd try to find someone who does race bikes, because he wouldn't survive if he wasn't good. Something that might be good to know: when the club shadow was dyno'd, there was very little difference between the sniffer results on individual pots, and on both together.