1993 Mercury Topaz Alternator won't charge battery.

I took the alternator out and had it checked and it pass with flying colors. I put it back in and it won't charge the battery. The battery is brand new. I was told there was an inline fuse in one of the wires coming off the alternator. My question is: Does anyone know which wire has the in line fuse and if I cound possibly run a jumper wire directly yo the Battery to by pass the fuse?