After an engine swap I had a check engine light and Restricted Performance message. I had numerous fault codes which I cleared, but I still have the check engine light on and Restricted Performance message. I checked and I do not have any new fault codes. I do have a battery not charging message with red and amber warning lights. I also have the ABS light on.
I have 13 volts on the amp gauge with the engine running.
Thanks for your help.

 

You should check the voltage with a proper volt meter while the engine is running but 13 is not enough. You should see at least 14v with a good alternator, usually a bit more than that.

 

I have 14.3 volts with the engine running at the battery, for some reason the gauge in the car reads 13 volts. Thanks

 

See if fuse #2 in the left side engine compartment fusebox might have blown.

If not, check the white-blue and the yellow wires at the alternator which might have been detached or damaged during the engine swap.