You said you'd gotten "hard disk not found" errors intermittently. A properly functioning player will never, under any circumstances, show that error message. So I think a certain number of your glitches are very likely a disk drive or disk connection issue.

It's true that some of the glitches could be in the source files themselves, so it's good to check them out. And the silent bits at the end of some tracks could very well be the source files. But since you also got the hard disk not found error, I wouldn't count on all the glitches being the source files. You're not gonna get that lucky.