Jonathan Gonzalez

I have a 2009 Mustang GT. My issue i'm needing help with is the alternator not charging the battery. i have done all my research on the subject before coming here to ask for help and this is what i have done/ checked.
Checked wiring from alternator back to pin 5 & 13 for conductivity at pcm. the yellow/ light blue had a short.. i cut it out and replaced the wire. no luck...
Checked for voltage at the alternator on the main power wire and the fuse wire. even did a load test on the fuse with a good extra blower motor i had and it worked no problems.
Checked and cleaned all grounds on battery terminal and the two that go to the back of the block and also where the alternator touches the block... did a ground test on the alternator case and was good... .0 while not running and .3 while running.
So i replaced the old alternator with a new one and even had it checked and tested good at autozone..
Tested the battery and that was bad so i put a new one in as well and after all of this i'm still only getting 12.5V while running.
The pcm and fuse box has been relocated so the ford i have it at wont touch it..
Any help would be greatly appreciated.