Volkswagen Repair: VW battery problems after alternator installation, vw golf gl, remanufactured alternator

Question
I installed a remanufactured alternator in my 2003 VW Golf GL (2.0 L engine, 90Amp Alternator).  Everything seemed to go ok.  Battery is only a year old, if that.  I disconnected the negative, took off the belt, took out the alternator, put the new one in and reconnected the belt.  I hooked the battery back up and noticed that a nut was missing from the negative side of the battery and that the terminal was not tight, but the car started right up, drove around fine and I thought all was good.  For 2 days the car ran fine, then today, I noticed that if I turned the car off, it would start back up again fine, but that my electrical components had been reset, such as the clock and my radio.  I decided to find a nut to replace the one that was missing.  Since I replaced the nut, the car didn't start.  I couldn't even jump it.  So I called AAA and he got it running, he even tightened the negative terminal moreso than what I could do.  I let it charge for about 30 min. and then as I was driving around, I noticed that if I lowered or raised my electric window, the dash lights and my headlights would dim and the second I stopped with the window, the lights would come back full force.  I parked and tried to see if it would charge some more, and it just shut off to where it wouldn't do anything if I turned the key.
Any suggestions as to if this problem is my alternator or my battery?

Answer
Oh boy, Erin;
When you change an alternator, put the battery on a charger while you are replacing the alternator, otherwise you run the risk of ruining the brand new alternator, because it has to immediately recharge a battery that is low.  That means "full fielding" the alternator, and that may be for a while, and the alternator's regulator circuit just can't handle that much current for very long.  First, take the battery somewhere where they can test it...I mean "load" test it.  If it is weak, replace it.  Then be prepared to replace the alternator too.  The same place that will load test the battery should be able to "output" test the alterantor too, so just take them both to the same place.  I'm sorry to hear about your trouble, and the extra expense.  But you know this for the future, and can probably save some of your freinds from the same distress.  Wish I had a better prognosis, but I'm afraid that they are both "toast."  Good luck, Erin.  I hope this helps.