Personally I think it'd be easier to just insert a new track (or use the insert synth dialog) instead of cloning then if you want to use the same MIDI clip(s)/data copy it into the new track.
Otherwise you gotta fiddle with routing and all that other wackiness.
That of course doesn't copy effects and whatnot over so that might be the issue.
Looks like the actual "clone and reroute" aspect has been covered though.
Cheers.