Hi Coach,
Can we ask a few questions first ?
Did you examine the plug that goes on to the alt carefully for any possible problem?
Does the fuse blow with the alt unplugged?
A wiring diagram in this case (direct short causing fuse to blow) will only show where the wire orignates and ends.
Replacing a wiring harness can mean a lot of unnecessary work whereas actually tracing the wire from the alt to the fuse panel may provide more direct results.
A wiring diagram may or may not supply the color wire involved, but that can be found right at the alt.
Two of the 3 wires go to the PCM and the third is the fused wire from the fuse panel .Easier than replacing an entire harness, I would remove the fuse panel get the color of the wire the fuse is supplying and go from there. . Sometimes it can be obvious with just a visual check, always a good way to start.If there is a direct short to ground, you might be able to notice anywhere that the harness can rub against any metal and that would be the first place to check.Do you think you want to try this path?

 

i Have looked at the plug. I did not see any visible damage. I will try and trace the wires from the fuse back to the alternator. Thank you very much for the help

 

Your blowing the 30 amp?
If you cant pin it down to wire chaff etc,, in front of the wiper motor/ left side rear of the engine is the regulator input from the battery junction box (30 amp protection).. Its a single wire connector, yellow/white.. If unplugged, does the fuse hold? You can also ohm test from the alt connector to this single connector for any short. Could be the new alt is internally the cause...