[DannMann99]

...maybe you fried a wire, and the clicks are coming from a gap in the wire and making a spark which could be unsafe. I'd check out how much power my alt was putting out, and id check the battery too, since you replaced the alt it should be running at normal, so if its coming up as not having a full charge, then its probably a wire thing. how hot is the alt becoming. also, are you sure the wires are in right on the alt. there should be (atleast in my car) 2 wires coming out of the alt, one i believe is the ground and the other carries the charge out. make sure the ground is on correctly.