My first guess would be that: You think from the "noise" that the computer has shut down, but it hasn't.
The likely condition is that the system is running disk repair trying to sort out something it doesn't like about the files.
THAT is why substituting a different HDD "cures" the symptom.
You need to sort out the issue(s) on the drive - maybe even going beck before the update and doing it over again.
This, of course, is where the smart-ass at OS9Lives (me) says… "You DO have a backup, don't you?"
Actually, although I NOT 100% certain and it may have just been a dream, I seem to recall more than a few people having issues going from 8.5 to 9.0. back in the day.
It was a major upgrade after all, and did not always go smoothly. This may just be a "If at first you don't succeed…" situation.
That said, there are certainly folks around here still familiar with the minutiae of that transition far more than I……