Performance issues can be tricky to track down.
Clearly you've spent a lot of time reviewing the hardware size of things. Assuming your HD is OK.
In some cases it's the fragmentation of the files and/or lack of free space on your HD that is more likely the issue. There are free apps to clear out old cache files and unneeded files. You'll need to buy a defrag app to defrag your HD or using an external HD you could copy off your internal HD files completely, then deleting your files from the internal and copy back your external HD files (a poor mans defrag).
You could also have something running in background that is sapping your CPU which will also slow your HD responsiveness. One common thing I look for is P to P apps these sharing Apps tend to kill your systems performance as people are accessing your system concurrently. I would turn off and disable them.
Malware is also a big problem right now some echo your actions and files to there servers (stealing everything from your system and life!) Make sure you have run Apples' OS updates as they have fixes to stop these and an anti-malware tool to remove some if found. It's now time to be more pro-active using an anti-virus program (which can also clean these Malware and worm apps).
You may also need to also check your OS & web browser of extension apps or widgets that could be running using up your systems resources.
If you have set some apps to start when you boot up your system you may want to disable this feature.
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