This is probably a dumb question but if you take the Cat out will it throw a code on the bike?
It probably will not throw a code. BUT! You greatly reduce the back pressure so the bike should be re-tuned to match this set up. Or you run the risk of improper fuel mixture and some damaged heads.
When i cut mine I cut it half way around with a grinding cut off wheel and then turned it over and stepped it over width of the wheel and cut the other half so it made a "Z" on the pipe. When I welded it back up held it at the "Z" part together and welded it back up. No alignment issues at all with it having a clocked position to reset to. Now if It was cut completely in half one shot thru then yes I could see a alignment issue.