You can polish off the rough spots with a very fine sandpaper (about 400 to 600 grit). Or a buffing wheel. That's what we use at the shop. Also, there's a needle hole file that can be used to clean up the inside of the hole. Your shop should have done that for you.
The biggest problems we've seen at the shop with these Jukis is the cutter. It can shut you down when it's damaged. There have been a couple machines, where we've just removed the cutter and it has improved the stitch quality. I know... we really love our thread cutters.