There are a lot of places it could go bad.

12.5 is not really charging. Should be around 12.8 or higher to even remotly be considered charging.

At rest with nothing drawing a good battery should put out around 12.7.

Put a 12 gauge wire from the back of the big bolt on the alt directly to the battery and see if you start charging. This will show your components are good. If not then you have some replacing of parts to do.

If it does charge, then you have to trouble shoot your wiring.

First measure your battery voltage.
Then with the key in run, measure the voltage at the VR and the back of the Alt.

Start the car, measure the battery voltage.
If everything works, then your bulkhead is getting voltage into the car, but the question is is it coming out.

Next you have two big lines coming out of your bulkhead connector. check for voltage going in and out. If it isn't making it out, it is either your amp meter, or the bulkhead connector.