I'm noticing a rough spot when decellerating at ~5K. I remember my GSX-R600K2 used to do this before I did the TRE mod. Is the timing on the GSX-R750K6 still retarded? If so, can this be overcome by remapping the timing with a Power Commander instead of the TRE mod? The TRE mod will kill the gear position indicator and I'm not sure that's the way I want to go.

You could always install an APE cam chain tensioner to keep things lined up on a closed throttle.