starter wires

Ok i have i 94 formula with a 95 engine in it. i had to replace the starter. I took off three nuts to take off the wires to it. now when i put the new starter back in the new starter only has 2 places for wires insted of 3 like the last one. also i now can not find the third wire i pretty sure i pulled off. i did have just 2 wires connected and car started just fine, but now ther is a short in the amp power cord. it blows the fuse in the cord even when the car is off. is this b/c of the "mystery" wire? or am i just going crazy :)? help!