I ran stock pipes all last year and anyone who has ridden my banshee would tell you its fast. However, when compared to other Banshees who have aftermarket exhausts, its slow.
The Banshee motor is based on the RZ350 racing engine Yamaha developed during the late 70s for GP racing. Yamaha does three things to make the power manageable for sale to the general public: the timing is changed, the air intake is reduced, and the exhaust flow is reduced. So, get a timing plate that advances the timing to wear it should be, open up the air intake to let it breathe in more air, and reduce the back pressure to allow better breathing and you will have a fast bike.
You don't need a new exhaust. Buy a used one that is clean. Those are a lot more plentiful and you don't have to worry about it bolting right up, (someone has tested that for you) I bought a Pro Circuit exhaust for 75 bucks and blasted and coated it for less than 200 out of pocket expense and I couldn't be happier. If you gotta have chrome then you won't have as many options, but you can still beat a new outta the box price for sure.
Pipes make the difference. Also your air box and timing do.