Too bad you are having issues. While the tasks you have done are good, there is actually more you can do. I'll make a few suggestions, along with making some other remarks/questions:
1. Are you making backups to an external device? If you are, what software are you using for that?
2. Do you do any of the following disk cleanup:
A. Remove files/folders/etc. that you no longer need?
B. If you have removed any apps, I suspect you just dragged the app to the trash. While that is OK< that actually does not get all the stuff associated with the app. An excellent freeware program that you can use to provide more complete removal is AppCleaner, available from here:
https://freemacsoft.net/appcleaner/
3. An excellent freeware program is the venerable Onyx, which you can get from here:
https://www.titanium-software.fr/en/onyx.html
Note that there are specific versions available for each Mac OS, so make sure you download V2.8.9.
4. While this free stuff is good, it would be wise to invest in a good commercial product. A very, very good one that has been around for quite some time is Tech Tool Pro:
https://www.micromat.com/products/techtool-pro
I use it every week for both of my Macs (and also Onyx), and I would not be without either one. The normal price for it is $99.99, but for the next two days, it can be purchased for $39.99:
https://shop.macworld.com/sales/tec...rsion&utm_content=techtool-pro-9-full-version
5. One thing that could be an issue is that the internal drive inside your Mac spins at a slow 5400 rpm rate. I am wiling to bet the drive has never been defragmented/optimized, both at the Volume and Partition levels, and for both Volume and File Optimization. Tech Tool, pro has those features, and when I had Macs which had HDDs inside, I used those features, and it made a noticeable difference.
6. How much free space is on your internal drive? That is important.
7. Finally, is all your third party software up to date, and compatible with OS 10.9.5?