Cat agressive to other cat.

We have 2 spayed cats. We had the first cat for about 3 years before we added our second one. Kept them separated for the first 2-3 days, and then introduced them slowly with supervision. They got along ok then and would even sleep together at times. That was 2 yrs ago. Starting about 6 months ago the older cat started being agressive to the younger one. This has progressively gotten worse. She'll go out of her way to stalk and attack the other cat. I've tried clapping, yelling "no!", and even a squirt bottle. We recently had the younger one spayed ( I know, we waited longer than we normally do but her sister died on the table during her spay and I was a little skittish that it would happen to her). We were hoping this would get rid of any female hormone scents that were threatening to the older cat. This didn't work either. They are both very sweet cats and I hate that they aren't getting along. The younger one stays hidden a lot now because she is afraid of the other one. I would love some help on this, but I hope it is not too late as the younger one starts growling as soon as she sees the older one getting near her. I'm worried that I won't be able to get rid of that 'fear' factor. I grew up in a home with multiple cats added at different stages and never had this problem before. In addition, one of them has started pooping outside of the litter box in the basement. We clean them every day and have one upstairs and one down. Haven't caught the 'culprit' yet.
Thank you for any help offered!!
Additional info if it helps: Both are indoor cats. Both are vet checked and healthy. We also have 2 dogs that the older cat doesn't bother. The cats ages are 5+ and 2+.

What you are describing often happens when one of the cats is sick (usually the victim of the aggression, but sometimes the other way around). Have you described to your vet what is happening to get his/her input? I can't but wonder whether one of the cats has a low grade infection which is causeing the aggression and the potty problems.

Hissy suggests a wonderful book for situations like this...and I can't remember the name right now. I will look and post it ASAP.

Here's the name of the books from an earlier post by Hissy: Pam Johnson-Bennett's book HissNTell and Cat vs Cat- both give excellent advice to mulitcat households.

Thanks lotsocats. Both have been to the vet recently and are healthy, so I don't think it's a matter of one being sick. I will check on the books. I definately need to find something to help this problem before the younger one gets hurt. Thanks again!!