The jetting was very, very rich for those carbs and I don't doubt it ran bad. That super rich jetting may also explain some of the smoke you were getting and the excessive wear you found once you took it apart. Very rich jetting like that can wash the oil coating off the cylinder walls, causing smoke and excessive wear.
I was also going to explain the large change in pilot jet sizes as well. I wondered about that too when I first started studying these carbs. I mean, it was basically the same 650 motor throughout the production run. Well, if you study the pic of the two different float bowl types, that explains it. It has to do with how the air is fed to the jet and what the jet flows. The smaller sized VM22/210's (sized in the 20's) flow straight fuel and the air is added afterwards to the top of the jet. On the larger sized BS30/96's (sized in the 40's), the air is delivered to the bottom of the jet and mixed with the fuel before the jet meters or flows it. So, the VM22/210 flows straight fuel and the BS30/96 flows the already made up fuel/air mix. The resulting strength of the fuel/air mix that gets delivered to the pilot circuit ends up being about the same, it's just done in two different ways.
Now let's talk about the jetting you may need. Looking at that chart I made up, you can see that the stock 122.5 mains are the smallest put in any 650 carb set, and by several sizes. They do work fine on a totally stock machine but are easily outpaced if you make any mods. Now I understand that your machine is mostly stock but it looks like you have the freer flowing Commando mufflers on it. That may require bumping the mains up a size or two. Only running the bike and experimenting a bit will tell you for sure but it wouldn't surprise me if you needed bigger mains. Also, one of the first rules of jetting for mods is that when you think you're good, try the size above and below that to be sure. So, I would get 122.5's and 125's to start, maybe 25 and 27.5 pilots as well. If you end up several sizes up on the mains, that may make the upper midrange too rich and call for leaning the needles a step. If you do that, it could create an off-idle flat spot and that would need a larger pilot to correct it.