Solved Charging problem after engine swap

[newstylecustoms]

I just finished installing an 04 Ranger engine in my 99 Explorer(all the wiring is from the 99), runs great. However the alternator is not charging properly. It never puts out above 12.5V so when I checked voltage at the battery running it was 12.5 engine off it was 12.4V. Before I pull the alternator I just wanted to see if anyone knew of anything that could have been missed with the wiring that could cause this condition.

Thanks

 

[newstylecustoms]

BTW this problem went away after the starter failed and I replaced it. I am guessing that is was a bad ground causing the issue all along.