My Goldeneye ghosted a bit with LEDs too. I'm pretty sure I had cheapo LEDs in it ... can't remember anymore.
Make sure that the ball save works correctly and the flippers are strong enough to hit that leftmost ramp shot the whole way around. The satelite toy and corresponding ramp can be problem areas as well. You want to make sure your satelite magnet is good and strong. You also want to make sure that ramp pops up when it's supposed to.
My friend had a GE whose ramp wouldn't pop up because it was really humid outside. The playfield wood had swollen and something was out of alignment. But, the problem went away as the humididty subsided.
These problem areas are probably ones you want to test with the glass off as they arise when you hit a difficult shot.... not always easy to do when you're playing for real!