Alt. Not charging and will only run at idle . It's also flooding

What is your question?

I have had the alt. Bench tested and it's good . Battery light is on in the dash .it's smoking black smoke due to flooding. Will only run at idle . Have replaced fuEl pump. Mega fuse is good and all grounds and fuses . This car did fix itself for one day,and went right back to doing the same stuff. There is a culprit for all these problems just not sure what it is . I do know pcm cotrols when the,alt. Charges . The pcm is 250 dollars and I need to make sure it is defected b 4 I replace . Help me please