I believe it would be a really nice idea to back up the data stored on the drive until you sort this out.
After that, you can run both short and extended DLG tests on the drive: http://products.wdc.com/support/kb.ashx?id=pyJxL3
Apart from that, I would agree with ko888. You can downclock the system and see if the issue persists.
Also, you can go to Resource Monitor and see if you get high disk usage.
In Windows 10's Task Manager click on the Start-up tab and see what the Start-up impact of automatically launched applications is having on your start-up process. You can disable or re-enable apps to test if they have any effect on reducing your start-up time.