#3 Cylinder Misfire on 2003 Pontiac Vibe

Trying to work on my friend's 2003 Pontiac Vibe after she had a complete engine failure. We replaced the engine with a salvage & had it running fine when it was up on jacks. After it was let down, however, it ran for a few seconds, died & refused to even turn over. We found & replaced a blown AM2 fuse & found the wires to the Cylinder 3 fuel injector were pinched & shorting out on the engine block. Clipped & rejoined the affected wires but now, we have a check engine light & it is giving a code for #3 cylinder misfire.

We checked power to the spark plug & coil pack - all fine, the fuel injector plug has voltage but the #3 injector is still not squirting fuel. With the fuel rail out, we swapped the injector plugs over & the problem follows the #3 plug.

Could the #3 cylinder injector wire getting pinched & shorting out on the engine block have turned something off in the computer, maybe as a safety? And if it has, how do we turn that cylinder back on?

Thanks & I hope someone out there can understand at least some of my ramblings. LOL