If you don't get both fins perfectly aligned it will do some weird stuff. I preferred running mine with just one fin (starboard) side after much testing. The boat does tend to chine walk a bit at high speeds, since it is a high lift design, but it handles very well despite that. It's really not a problem most of the time.
I ran my rudder full length... can't really remember exactly how deep, but I'd say about 2.5 to 3" below the drive.