Stock exhaust systems are carefully designed for good performance for a particular engine in its application. Putting one from a different motorcycle on, which has larger tubing of different lengths will almost certainly compromise performance enough to notice. Unless you just changed the last part near the muffler after the collector, that is. That may not hurt much.
When I got my Moto Guzzi 1000 I used an online exhaust system design web page to design a system from scratch. After entering all the data, including redline, displacement, cam timing, and other things I don't remember at the moment, it spit out numbers that were very close to the stock system, including tubing diameters and lengths. I decided not to try to make something "better".
To answer your question, I'd use a hack saw.