My factory setup is 80 Pilot Jets and 160 on the main jets. I'm not sure the valve spring metering. It is the stock air box as far as I know. Ill look into it and find out.
The weaker the spring, the more fuel you get on the very low end, it keeps the carb from flooding at idle, basically. The black spring is the 80gram spring, and there are two silver springs, one is 95grams and the other is 65grams, I think. The 95gram spring is wound opposite all the rest, a total of four are used in these carbs.
Do a yahoo search for mikuni super bn carburetor manual and you'll find the basic manual explaining which parts are available and their basic function, some of it is a bit awkward b/c it's translated from Japanese and I disagree with small parts of what they say but for the most part you'll want that manual.
For component selection, it's best to start with confirming the factory setup and making sure your carbs really are clean and the pump is in good condition otherwise the tuning process will take longer. Check your cylinder compression as well of course, so you'll know where you are on that.
I have #80 pilot jets in mine now, and it's plenty rich in mid range so I think that sounds okay, were your diaphragms in good shape, almost as soft as rose petals and no holes in them? Are you certain you hosed all the gum out of the transition ports ("bypass holes" mikuni calls these), do the idle mixture screws seem to work properly, sometimes you can get a tiny amount more fuel out of these without affecting idle quality much. It all adds up, I'm sure you already know.
As far as the water leak goes, it could be coming from a lot of places. Often from where the drive shaft goes through the hull at the carbon ring (fragile!) the rubber bellows loses tension and the carbon ring wears egg shape inside and doesn't seal well with the rotating stainless ring. Or, you might have a leak somewhere in the exhaust system, since it's water jacketed and the tuned pipe has an orifice where water is injected for cooling the pipe and changing it's sonic length, so you have to check all the stuff out, look for holes burned in rubber and plastic parts, etc., leaking gaskets(sometimes at WOT, they can spray water over your carbs, too).