On my 00 I did all kinds of mods on it and for the most part it made it less ridable, faster in a straight line but not very good leaned over, leaned over is more important to me. And being nice and quite so the piggys don't hear me is nice also.
It's still a very fast bike stock, and mine is bone stock, still has the rear fender in tact.
A friend of mine has one of the OG yosh boxs, he worked for yosh and is still involved so I know a bit about it, not braggin or tryin to be something I'm not.
The PC3usb is the best thing I"ve ever done to either of my Busas'. And the box mod is cool and all, gives it a bit more oomph but in real world testing the stock set up performed better, imagine that.
There are two things I would consider doing to my stock 99, one, a Ti akro system or Turbo. The Akropovic is the quitest of the bunch producing big tourqe improvment with the most weight reduction, so it would be worth the extra noise.
Turbo? run it thru a stock exhaust that was hogged out, turbos are quiet to begin with so the gutted cans wouldn't make it that loud and it would look stock...sleeper.
Only thing you would hear is the pop off valve.
I've tried using the yosh box and it didn't give the same results.
If it works for you, cool, I aint gonna knock it.
My .02.