Here's a link to Matt G.'s fairly recent dual battery setup we did for his SII (basically a stocker):
Project: Fireball - Binder Bulletin Forums
Scroll through the posts until ya get to the portions that deal with sparky stuff.
He's since corrected all the charging circuit issues regarding the bulkhead connector, etc. Part of the problem was also a "low output" alternator (common 10si issue) which has been swapped for a fresh QUALITY rebuilt unit. In fact...I VERIFIED that all is functioning normally now just this past weekend when we built a fresh carb for the ride and had Dave the Gear Man install a FRESH rear axle setup.