I didn't change anything except blocking off the PAIR hose. It pops quite a bit on deceleration if you don't do this, but it still runs just fine. My gas mileage has dropped a little, but I'm pretty sure that's my fault for playing with the loud handle so much.
It looks like the angle of the can is the same as stock, and the Scorpion is much shorter, so it might clear, but I'm not sure. I know Dale makes a sport touring can that rides lower for folks with hard bags. I know several others here have the Scorpion slip-on, so maybe they can offer some better advice regarding clearance.
Good luck.