I am speaking about GM 10SI. I am assuming that #1 and #2 have the same function as a 10SI. If a Geo has some goofy alternator, all bets are off. I don't have a 1998-2001 Geo wiring diagram to check alternator hook up.
From what Dennis said and what I have read, I'm sure that the Dennis has the Denso alternator, not the Delco SI. This makes sense since the Geo is a Suzuki in disguise. The Denso wiring is different than the SI. I'm guessing that if you wire the Denso up like a SI, the current will flow through the small jumper causing a drain on the battery at all times. Dennis already proved this with his ammeter check.
Dennis: sounds like you are close to figuring this out. Looks like an interesting alternative to the SI
This might help:
Toyota (Denso) alternatorDisclaimer: I haven't wired up a Denso myself; just going on what I have read.