Alternator?

[MSP09]

My alternator in my car is wired a really confusing. By the stock wiring diagram the connector that goes to the stock alternator has two wires and that gets connected to the alternator by a connector. The way that the car is wired right know is thet one of the wires is spliced with a 30 amp fuse and is bolted to the alternator bolt. So that stock connector that had two wires that was connected to the stock alternator is only connected by one wire while the other is bolted down. The alternator does not charge the battery. We have also returned the wires back to the way they were supposed to be and no luck. Please can someone help? I will try anything, the car does have a LT10 Microtech. I will try to post a picture later but if I have explained it good enought and you all can help that would be great. Thanks all.