Glad to hear it helped. You should know that there are a few parts that folks have issues with using HLE in WW. If you come across the issue again, try switching back to LLE to get past the problem spot.
This kind of issue is why I asked RachelB to make the game's config force it to use LLE shortly before 4.0. GOOD THING NOBODY USES ANCIENT BUILDS OF DOLPHIN TO PLAY WIND WAKER
Also, don't use save states on Wind Waker. There's a pretty easy way to corrupt your memory card save with those, and making them under HLE can prevent you from just progressing with your save states. Memory card saves almost never have issues.