I know this is going to sound sooo obvious... but sometimes it's the first thing over-looked and the most common problem.
Take the battery cables off the battery and clean them "good". (Not just the part you can see, but also where the wires are attached to the clamp.)
Next, have the battery checked by a professional with a meter. (Auto Zone, Advance or even Wal-Mart will usually check it for free... they sell batteries that way!) It's best to let them check it "on" the car and "running", if possible.
I don't mean to sound condescending, but once I returned an altenator "three times" and almost had a fight with the store manager because I believed each altenator that I installed (all rebuilt alts) were bad! It turned out that the connection "inside" the cable/clamp wasn't making a "good" contact!
Anyway. it's worth a try!