Looking at your data - your storage has to be performing horribly.
- SSD HD: 245/249.77 GB Used
To fix this:
- Make a bootable backup and test it (or make sure your Time Machine or off-site backup is solid and you know how to restore / how long that will take)
- Make a new user account
- Delete your main user account and let the Users & Groups preference pane delete all your user files.
- Boot the mac into recovery and run disk utility to check the directory structure and most importantly - allow the unused blocks to be trimmed. (alternatively you could boot into single user mode and run fsck on the unmounted volume. That trims unused blocks equally well)
Once that is done, start up the Mac and log in to your new test account.
Collect timing statistics on what you wish to benchmark. Make sure you have repeatable numbers (maybe run 5 tests - see if you have to discard high/low values - if so, better to make 10 measurements).
Now that you have a solid benchmark of how the software performs with enough space on the drive to arrange the storage efficiently and for rapid read/write performance, you can contemplate moving back some or all of your user files from your backup.
I like to keep 50 GB or 10% of free space on my SSD - whichever is the larger amount for maximum performance. Any less than 6 GB free + size of RAM is a danger zone and means I am sacrificing serious speed to have the drive that full. Get a 64 GB RAID USB flash drive for $20, or USB SSD or spinning HDD to hold your large files and you will probably have to do nothing else to speed up your Mac.