Drill out the air/fuel screw caps and set the screws to 2.5 turns out (may have to turn them out a little more for best tune) . Mine were set bad at the factory, from almost closed to two turns out. Set them all the same. Then get some washers from radio shack and shim the needles. I'd just get two #100 main jet and put them in 1 and four, two and three have 100's already. That will cost you about $20 for the two jets and bag of washers.
Thats just my 2cents,....hope it helps
Pretty sad that your bike came with those crummy settings! But, what the hey - we can feex them, no? You seem to have a running start on this problem already.
Just for the record, the '99 B12 came with the following size jets: Main: #102.5, Pilot: #37.5, Pilot screw: "Pre-Set" (whatever that means). Having done some rejetting before, it turns out that these jet size specs are just "jumping-off" points (baseline settings) and there's usually a lot to be gained by the do-it-yourselfer in the way of HP, economy, and rideability. Mikunis are easy to work on and parts are readily available. Good books are also available on Mikunis.
Since the engine runs lean on both ends of the RPM spectrum, it pays to retune for better rideability by correcting the A/F ratio off idle with the pilot screws and by trying different pilot jet sizes and by improving the air and fuel delivery at the high end, starting with a Pingel shutoff valve in the tank. The stock shutoff doesn't flow enough at high RPM's. Then make sure there's enough air up there as well by yanking out the snorkel and/or making the 2"x2" mod to the airbox (pod filters look cool but aren't so great in the rain). If all this is done right, you probably won't need the Radio Shack washers.
You suggest using the same main jets on all 4 carbs. I seem to get better results by making the center cylinders one jet size bigger (richer) since the centers on air-cooled engines run hotter than the outer cylinders. You may want to experiment by buying 3 different sets of mains, starting with the size just above stock and getting bigger.
While an air/fuel meter would be nice, I want some day to get a set of thermocouples and a 4-channel meter so I can do some dynamic testing of the exhaust gas temps. Using EGT's would allow me to rejet until each cylinder is delivering the same torque under WOT. It's also possible to compensate for mechanical and wear differences this way on older engines. There's a few tenths to be gained there, I think. The idea is to get all four cylinders to do the same amount of work.
Anyway, I'm prolly preaching to the choir here. Good luck!
Herb