Endless Beachballs and Random Freezes

[ildondeigiocchi]

The issue I'm having is very weird taking into consideration that I just upgraded my hardware two months ago. I have an Intel X-25M SSD as my boot drive for OSX and a 1.5TB WD HDD with my Home Folder on it. Whenever, I launch an app it never launches immediately. I get a beachball that lasts about 5 seconds. When I try shutting down the computer I have to hit shutdown about 3-4 times before it does. Otherwise, it warns me with a message thats something like this: System cannot logout of user account because Safari is still in use. (but it's closed). Launching an app from an ssd should be instantaneous. So I don't understand if it is a hardware or software issue. I reset the PRAM ... helped for about a day but I'm back to the slowdowns. Any ideas.

Also when I performed a software update for iTunes, the update installed but I got this warning so I have a feeling something is wrong.

 

[Transporteur]

I have had some similar issues with my MacBook. Continuos beachballs, especially in Safari. All updates Apple provided and resetting the system in all possible ways did not solve the problem, so I ended up making a clean install.
Till now, everything works fine.

 

[ildondeigiocchi]

I have had some similar issues with my MacBook. Continuos beachballs, especially in Safari. All updates Apple provided and resetting the system in all possible ways did not solve the problem, so I ended up making a clean install.
Till now, everything works fine.

How can I do a clean install taking into consideration my HDD setup.