The pipes that have been mentioned above will all work great. PTRs don't have the RPM range to handle an RZ top end well. I used them for about a year, it will be the smoothest a Banshee will ever get. The Rockets work well and clear with no problems. Most pipes can be cut and turned to clear.
rzcolo has Toomey T-3s on his that have been cut to fit. I may have a set of Rockets for sale if I can find out if Shearers will fit.
It kind of sounds like an ignition issue to me too. Plugs look OK, right? Try to swap out the coil first, they are all the same. It's an easy one to start to rule out what could be the problems.
I'm kind of in the same boat. After ALOT of shopping, a 400ex looks to be the winner here. Safe, reliable, boring, smooth, easy to ride bike. The Blaster is a close second though.
I've got one. The front end looks great, but the subframe has the look of a previous owner that wasn't very good at wheelies. It is bent up at the back, but could probably be fixed.
I have a set of perfect cases, a stock stroke after market crank and stock cylinders. The cylinder are at 64.50 I beleive and will need a bore, but you can have them pretty cheap.