If you don't mind pulling the whole exhaust off the bike, cutting the breadbox and welding it can be done successfully. Just cut a three sided square hole and bend the metal back so it'll go right back in place.
The problem with monkeying around with the exhaust is the velocity needs to be maintained for proper low RPM scavenging. Pipe length is important. That is why I'm adding the dan moto can on rather than just an exhaust tip.
I'm going off the theory that Kawasaki put some thought of the exhaust flow when they designed the pre muffler, though sound reduction is probably higher on the list.