Check charging system
 

2weeks ago I changed the battery and alternator on my 06 SEL. Ran great no issues til yesterday. Got a check charging system notification and a battery light. Had it checked at advance and they show no issues with charging and no issues with the battery. Still have this notification that comes on 30 seconds after I start the car. They also checked for codes. There were none. Any ideas?. The alternator was a remanufactured unit under the Carquest branding. They said they will replace it ,but it was a real PITA to replace so I want to troubleshoot it 1st. Anyone else have this issue?
Update. Now the car stalls at traffic lights. RPMs immediately drop to 0 and stalls out. Have to shift into neutral and give it gas to keep it at 1000 RPM. also has a hesitation when applying the accelerator. All of these are new symptoms since the Charging system notification.

After researching, I found out a few things that may be helpful. The Ford alternators are smart alternators. They send and receive signals from the car's computer. From what I found. Many times the companies that rebuild alternators don't always get the electronics right. I believe that was the case for mine. The people at advance auto were very helpful . I had decided to go for a new ( not rebuilt) unit, however advance auto does not offer one, so I elected to replace it with another remanufactured unit. ( They have a lifetime warranty) Took a little less time replacing it this time than last as I had a better idea of how to do it . So far no issues.