I need some help with a charging problem on a 04 gt

I have looked thru the threads on here and found some good information, but nothing has worked! Okay, here is what is going on and what I have done. I have completely rebuilt a 04 gt that I bought wrecked. I did an engine swap, added long tube header, EVE intake, cold air kit and car has x pipe with PIPES muffler. I put a 130amp alternator and a 765cca 95r battery.
Car cranks, runs, but the alternator isn't charging. I have what appears to be dead short somewhere, but where?
Battery is full 12,5 amps, as I said brand new alternator (tested good off the car). Battery light on dash is on. Check voltage on Alternator connector on top connector 0. Take ground off of Battery, put probe on ground post and then the alternator reads 12.45? I have traced the ground from the battery to the block and it looks fine. Traced the positive all the way to the starter, still nothing.
Next, did a fuse test with with test light, power to all fuses and all fuses good.
Then I decided to check for parasitic drop, took ground off of battery, hooked up DMM and DAMN IT, 12,4v on volt side and 0.15amp on other. Like I said before, touch probe to ground post of battery with out the cable and the power goes to alternator.
ASK me any question and I will try to provide what I have done.
HELP!!!

Okay, once the K-member was reinstalled after the long tube headers I was able to connect all the frame grounds. I have checked to make sure all the grounds are connected. I did a continuity test on all the fuses like I said, from ground to hot, everything is showing connections. I haven't done a key on test for 12v. The thing I don"t understand is, when I have the ground strap of the battery, reading from the negative side of the battery post to the alternator is 12.4 but the ground back on and it goes away.
Any idea's .

thanks,
Russ

Oh, I meant to mention the large wire on top of the alternator show 12.4 when ground is disconnected and I do the voltage test from the ground post. WHEN both cables are on the battery nothing on the alternator?

Thanks for the information, I will try the key on test today.

Oh, one other thing I forgot to mention. I replaced the factory fan with twin electric fans, not sure if that has any impact or not? The original radio was missing and replaced it with aftermarket blue tooth radio.