Yup - raise the bike back up to stock height if you can. Honestly, it will handle way better and chances are the loop at the back will cease to be a problem. If it's going to 'look' like a cafe racer, it should be designed to handle well.
Nothing wrong with slammed bar hoppers, so if that's what you're going for then maybe just go up 1/2 way back to stock and/or angle the loop. But with the styling I'm seeing, 4 into 1 pipes, 18" rear wheel etc, I'd go the 'performance' route vs. a low-slung straight line hauler.