I’m gonna go out on a limb here and say... I think you have more than one problem.
Yes, the plugs are a bit darker than ideal. But not to such an extent that oil burning would cause a misfire. The smoking exhausts also point to oil being burned, but again, not to the extent it would cause a misfire.
A sticking valve might cause a misfire / very poor running though. You could take the exhaust pipes off and have a look up in the ports with a torch to see if the ex valves look particularly carboned up.
It would be a heck of a shame to spend a load of time and money rebuilding the top end only to find it still has a misfire when you’ve done... that would NOT be good for the soul! So I’d definitely test out both carbs one at a time on your single carb manifold, before stripping the top end, if I were you.
It‘s kinda difficult to understand what someone means by ‘misfire’ or ‘herky jerky’ etc via text, but generally speaking, such dramatic misfire type scenarios are down to either carb or ign 99% of the time IMHO (we’re not looking at a race engine and megaphoneitis here).
Its interesting that your misfire is at certain revs. That could link to certain vibration frequencies. That was the case when my Boyer back plate terminals broke and I was convinced my issue was carb related! I know your chirpy chirp was the left hand cylinder, but that’s gone now and the misfire remains, you can‘t tell for sure when riding which side is misfiring. In fact, if it’s causing a pronounced ‘herky jerky’ I’d say it sounds like both cylinders are misfiring. So you COULD still have an ign issue.
And although your carbs have been sleeved etc, you COULD still have a carb issue. I don’t know how you ascertained the pilots are clear? If it was by inserting wire or similar then they should be clear provided you used the correct gauge wire and blew them out fully afterwards. However, if all you’ve done is squirt carb cleaner through, all you’ve ascertained is that they are not FULLY blocked. You have not ascertained absence of a partial blockage that could effect flow rates. FWIW I chased carb issues for a whole season once only to discover it was machining swarf in the pilot jet, swarf from having them bored and sleeved! As already mentioned by a previous poster, the best way to diagnose carb issues is to mark your twist grip, you can then ascertain whether or not the misfire is related to a particular throttle position, and therefore a particular carb circuit. Revs don’t tell you that, at 3,000 rpm you could be at 1/8 throttle, full throttle, or anything in between.
Sorry for waffling on so long (lockdown symptoms) but I’m just trying to say that I think you need to do more problem solving BEFORE stripping the top end.
All only IMHO of course.