Good checks mentioned above. Also worth adding a ground wire to the VR case. Scraping a little paint off near the mounting screw works well.

If you do find the alternator is fubar then yes there have been lots of problems with reman squarebacks. Also you may be overspeeding the alternator if you are winding the engine up with a standard crank pulley (7" or a bit bigger). Somewhere around 15,000 to 18,000 RPM is redline. Depending on pulley ratio you may be exceeding that. A smaller crank pulley or bigger alternator pulley will slow it down and also reduce idle output. Depending on electrical needs, you may need a better alternator.