You may want to check out Cruisers ground refreshing list. I did an ohm test on one of my alternator replacements when it charged poorly and found a significant resistance in the ground circuit. Not enough for no charge, but enough for a poor charge.
It's also possible something is wrong with your battery.
Be careful tightening the yellow (I/F) and tan (L) wire studs on the alternator, it's possible to spin the stud and break the connection internally. I clean the studs and wire rings then just snug them, then cover them with a finger full of grease or dielectric paste.
Sometimes the connection studs are marked differently, the important one is almost always I, F or I/F.
Not beyond the realm of possibilty, you got a new alternator that is faulty or a return/rebox that the parts guy gave you.