My original OS is 10.10.5. I had trouble with really bad beach balling. I ran an Malware bytes scan, everything is good. I ran disk permissions in Disk Utility with a total of two repairs and verified after each repair. Verified a total of three times. Prior to verifiying it a third time I received a cksum error on both repairs. I erased the hard drive anyways because it was still beach balling and it went from 10.10.5 to 10.8. I ran an upgrade that took at least 12 hours to complete. It rebooted and it stilled continued to beach ball after the upgrade install. SMART status is verified so I'm assuming the hard drive is good.
Sounds like you have the 13" MacBook Pro 2012, Disk Utility is not indicating a failing hard drive via its SMART status, and that the OS and/or any software you are running is not the cause there is one other thing I've not seen you mention you need to check into.
This model MBP13 2012 can develop an issue with the flex cable that connects the hard drive to the rest of the computer if the unit is getting carried around in a back pack or heavy book bag. The cable can be damaged by compression of the bottom case in the area where the cable runs from the hard drive to the logic board causing errors in the integrity of the data flowing to and from the hard drive.
Check out Apple's website but for this model they may still be offering to replace that cable at no cost for the 2012 only. If you've never had the hard drive flex cable replaced then all things being equal that may actually be the cause. Failure of this cable/bracket assembly starts as a general slowdown of even the simplest things on the computer like just opening a folder full of files. Best of luck with it.