2003 Mitsubishi lancer

I just replaced the alternator in my lancer now it is overheating. If I bypass the fusible link on my positive battery terminal the car runs fine but that fuse is tied directly to the alternator so it drains the batter when disconnected. My question is why is overheating when that fuse is connected and not overheating when I bypass it? Is the belt not tight enough or is the link bad on the terminal ?