So i've noticed that lately just by looking at my factory volt gauge that if i'm driving at night with the headlights on that my Volts only read at 13.3-13.5ish. Before they were 13.7-14.0.. If i turn the radio or A/C on they drop even closer to 13. During the day not using the headlights or anything the Volts will be up closer to 14 again.

My question is, would rewiring the fuel pump possibly have made the alternator run lower volts like this?

I'm going to put a volt meter on the battery tomorrow while the car is running and see what that says because in the past a volt meter has actually read higher than the volt gauge in the car itself.

 

P=VI

your alternator is constant so P is the same.
your I (amps) went up, therefore your V goes down.