You have the advantage over me, you have access to the computer. From your posts this is what I have
Consistent report that the HD is bad
Clicking sound. Ticking or clicking is the traditional warning for bad HD.
Not being there, I lean toward a bad drive. I know that you took the HD test and all, but on one hand I have the HD test on the other I have the warnings and now the clicking. Seems like the HD malfunctions in some way after wake up.
Lets try this. It does not report on a bad HD, but it will tell if there is some OS corruption, maybe causing the bad warnings SFC /SCANNOW Command - System File Checker