Best to use some Apps here to do the job. But before you start make sure you have a good backup!

• I would start off with this: Disk Doctor It will do most of the heavy lifting here deleting your old files.
• I would then use an external bootable drive to boot the system up from so I could then use Apples Disk Utility to repair the permissions and the disk its self. You may need to run it though a few times to clean everything.
• The next tool here is a HD drive defrager (not needed with SSD's). It re-connects the file fragments back together as they do tend to get scattered around the disk more so when the disk is full.

The last thing I would do here is clear out any old files so I have at least 1/4 to 1/3 of the disk free. This will minimize file fraging and will offer your system needed swap space.

You may also want to think about upping the RAM to 8GB if it isn't already and review what is running within Activity Monitor. I would be careful here stopping or deleting processes until you understand what it is doing and which app it maybe part of.