If the following suggestions work, please let me know and you can Accept the answer (and if possible, leave positive feedback). If not, please DO NOT Accept the answer. Instead, let me know and we'll try some more things or I can refer you to another Expert who may be able to help you further.
Before we go any further, I would suggest you use a program like Carbon Copy Cloner (http://www.bombich.com/
) to create a restorable backup of your Hard Drive to an External Hard Drive. This free program will make a mirrored copy of your hard drive in it's current state that you can go back to if things go south after the following changes. I do this personally before I perform any kind of install, update or major change to my system.
There are a lot of things you can do... PRAM, Disk Utilities, Permissions Repair, er, wait, you've already done all of this... You seem on top of your game. The only thing I can suggest now, is create a backup of your hard drive with Carbon Copy Cloner to an external. Then run an "Archive and Install" of your system. This should clear up any problems you might be having. You won't lose any of your files, it will maintain your user folder and all your programs, just replaces the System Folder. I would do this, then see if the computer performance is better. Don't run any updates on the computer until you confirm that it is running beach-ball-free. Then run any Software updates available. If it's still beach-ball-free, then you should be good to go.
If you are still encountering freezes, then the error may be deeper. It's possible that it is a hardware problem with the machine. Unless the freezes occur when performing a specific task or running a specific program.
Regardless as long as you have a Clone of your hard drive on an external drive, you always have a safety net, a restorable backup so that you can undo anything you've done. Good Luck. Please let me know if you have any further questions.