HI Shawn. Internet Diagnosis? Could be a defective re-manufactured alternator. If you have double checked all the wiring and connections, and everything is hooked up correctly, then having the alternator tested would be the next step, in my mind.
Disclaimer - I am more of a shade tree mechanic, not a tech. So hopefully one of our tech members will jump in if there is a better route to go.
Keep us updated and good luck.
i have a 2009 Lincoln MKZ with the 3.5l AWD
we just did a engine swap and put a 3.5 from a 2010 mkz into it. Replaced the alternator with a reman alt but it still won’t charge the battery. It will start and run I even drove it a little bit it keeps draining the battery. We tested for a power drain but couldn’t find one. It’s like the alternator just ain’t charging. Any idea on where to go next?