Saroset

So, I got this EX about three years ago. After trying to find the source of a rattling noise for about six months, I figured out it was the alternator. Easy fix, I did a little reading and followed the chilton manual on changing it. The noise 100% disappeared and I thought I wouldn't have to worry about it for a good while. Two months later, the rebuilt alternator I got is now making the same noise. It's this horrible rattling/grinding noise I can hear over idle and light acceleration noise.

I went to check the warranty or O'Reilys and the guy behind the counter strongly implied that I probably installed it incorrectly, but I cant find any information on what I could have done wrong. Since this is the second alternator with the same problem, is it possible that I have some other physical or electrical error that is causing the alternator to go out? Is it possibly related that my low gas light stopped working around the time the first one decided to stop charging correctly?

On an unrelated note, does anyone have any links on rebuilding transmissions and can a manual from a same gen LX fit on and EX?