I am assuming you're running the latest firmware and all that. Did you use any of the commands in safe mode? Like Rebuild Database or Restore File System? Both of those should be tried if you're having performance issues.
You should try option 4) Rebuild Database
first. Here's what it does according to PS Support:
Deletes messages, playlists, changes made on [Information] screens, trimming information for pictures in [Photo], video thumbnails, video playback history and video resume information.
* This operation may take a long time depending on the type and number of data items.
All your game info, saves, account info, and users will all remain intact. It resets things like folders you've made, playlists will be erased, and video thumbnails and photo edits will be removed. Clearing this memory can help with performance. Games, saves, and account info is not affected. If the system gets stuck or frozen when trying Rebuild Database you might have a failing HDD, but run this first before jumping to conclusions.
Then you should try option 3) Restore File System
. Here's what that does:
Attempts to repair all areas on the hard disk drive where files can be saved. Corrupted data may be erased if it cannot be recovered.
If there's anything corrupted on the HDD then this will get rid of it. Once again all games, saves, users, and account info is safe. Stay away from the other options at this point
I do each one about once every year or so because it's the closest thing to a defrag you can do on this type of file system. When it takes a long time for the icons to load when I quit a game, or if Trophies take forever to sync, then I know it's time to run them again. Also, it's never taken nearly as long as the warning says. I've not seen longer than 15 minutes or so and I have more than 200GB on my HDD usually.
Hope this clears up your problem. If it persists after this you might think about installing a new HDD and starting fresh, just to rule that out. An extreme move but cheaper than a repair or replacement. Post the results as you go and good luck.