Hey Vee
I think our bikes are cousins! I purchased my 99 B12 a little over a month ago and been having problems with the carbs, similar to yours, right from the start. I also have been having carb issues. I thought my bike was stock when I bought it but I was quite mistaken. I figured it had a jet kit in it because of the 2" mod on the airbox. In the month I have had it, I have fouled 2 sets of plugs. 1st it was cylinder 1 and 2. Then after I synced the carbs it was 3 and 4. When I pulled out my carbs I found 127.5 main jets in it. I thought that was the problem at first because the bike had the stock can, so I complained to the dealer and he gave me some 112.5 mains to see if that would help. Well, after taking out my carbs, changing the jets, giving everything a quick clean, putting it all back together with some new plugs, cylinder 2 never fired. After going through a bunch of stuff like checking the coils and wires and stuff, I realized that I was flooding that cylinder like Katrina (intended for levity only). I wanted to check and see if my float needle valves were holding good so I put the petcock in prime with the bike off and the next thing I knew is that gas is pouring out the vent tubes all over my chain. Well, if I lived in the city, I would have thrown my self in the path of oncoming traffic, but I don't, so I had to be content with laying out a nice long string of obscenities.
My carbs are back out on the workbench again and I'm trying to really give them a good cleaning. The float needle valve seat is a pain to get in there and get clean, but I'm a pretty sure that is the problem. I think that may be the problem with your bike too. With these vacuum petcocks, fuel is only flowing when the bike is running. Fuel level in the float bowl is critical, escpecially if you ride like a normal human being. This seems like the most logical diagnosis for your bike as I am living with a similar problems. Also, if you want to check and see which cylinder is misfiring without pulling stuff apart is just when you first start it up, when the bike is cold, start touching the exaust pipes. The one that stays relatively cooler than the others is your misfire. I hope I don't need to put a warning on how hot the exhaust can get. Good luck on it.
Keep up the fight. My wife has already nicknamed my bike "The Dud"