Try turning the mixture screws a 1/4 turn in and ride around a bit, see if that cleans up the base ring a bit. The purple bits are usually just the crap they put in gasoline these days sometimes when I switch stations the plugs change colour a bit. Usually the base ring being sooty means that you need some more air in there so for fun try putting the stock filter in and pulling the snorkle or see if just a 1/4 turn in on the mixture screws help
From what I gather here on the board for stage 2 you need like 147.5's or 150's and Dales special needles. I hear that tuning a stage 2 is tricky, you may want to buy the kit from Dale as he will help you tune it.
http://www.holeshot.com/bandit/bndt_b1201_stage2.shtmlI think if you make the 1.5" hole on the top a little bigger it will probably clean up the jetting or alternatively just lean it out a bit. Taking out the snorkle to test takes all of 20 seconds to unscrew the two philips screws on the document tray and is easily reversable. If you take out he snorkle and find it too lean then you can just tape up tiny bits of the 2" snorkle hole until it's perfect, then at least you know sort of how much to enlarge the hole.
For example if the 2" hole was taped up a quarter that is 1.5" which you won't go past because that will be the same as having the snorkle in. So say you test the bike with the snorkle out and find it a tad lean, say you tape up an 1/8th of the 2" hole and now its perfect. So now you know that when you put the snorkle back in there you have to enlarge the top cut hole to 1.75" with the snorkle in. That way you get the best of both worlds, you have the snorkle velocity stack for lower end/low mid range torque but also have a big enough hole(1.75" in this example) for the upper mid and top end power.
Going to a stage 2 you will lose some low end as you basically just have the carbs open and the air isn't accelerated and smoothed out with a velocity stack(the snorkle). In an ideal world the intake would be variable like the fantail exhaust on a fighter jet. At lower rpm it would be smaller to give maximum torque but at higher RPM the intake would expand to allow more air for maximum horsepower.
Stage 1 is a comprimise between maximum power and low end torque, you get good numbers for both however you don't get theoretical maximum torque and you don't get theoretical maximum power. However for drive-ability the stage 1 is excellent and for %99.99 of people out there because chances are they aren't towing a trailer or wide open on a drag strip and it's still way better than stock at any rpm or throttle position.