The way I understand the working of the 90 deg V twin, and when I've watched the valve gear operating, this seems to be the case, the flywheel marks can apply to only one cylinder (which one I'm not sure, and my Workshop Manual says only that the strobe light should be connected to the spark plug, without saying which one). I have only set (and adjusted) my timing statically, going by the way the bike feels under power - when it feels good, that's where I set it. I have the Kokusan ignition.
I also have DelOrtos. If your DelOrtos each have the same jets and settings, I guess that's why swapping them makes no difference. I put a different idle jet into one of my carbs, and synced the carbs very carefully, which made it run really good. It was a long time ago, and I can't remember which carb I changed the jet in, and what size jet it was - sorry. But I reckon each engine has to be set up uniquely, anyway.