After running Norton Systemworks for about 7 hours, I have yet to hear the little ticking noise, startup took a normal time and everything seems to be running smoothly.
I had deleted a number of old OS 9 applications and files a couple of days ago, ran a fix permissions thing and then today I ran Disk Doctor and Speed Disk. First I did Disk Doctor and had to fix a couple minor issues. Then I ran it again to make sure no issues. Then came Speed Disk which took an awfully long time (2.5+ hours). Then reran Disk Doctor and got a clean bill of health. I had a little bit of difficuly switching back to booting from harddrive from the CD because for whatever reason the CD won't let me choose the startup disk and then the mouse didn't work when I tried to pick manually. But quick hands when ejecting the CD fixed that.
Now the computer is purring instead of ticking and I am happy for that.
Not happy about writing my report due in 18 hours that I haven't started. Should work on that.