Hey there joe5,
hear something shutting down and then winding down for a second or so
Or incase it is not the HD , something else that you can clearly hear shutting down and make a sort of winding down sound sound for a second.
This sound could only be one of two things, either the hard drive or the cd-rom drive.
You can try unplugging the CD-ROM and see if you still hear the noise but in all honesty with the other problems you are having I would have to say that I think your hard drive is on the way out.
I know you have said that you have run some programs to check the drive health but those tests normally check the physical health (e.g bad sectors) it can't actually check the inferface/power side of the drive.
I have experienced problems like this with hard drives before and after installing a new hard drive I have had no problems.
You could try changing IDE cables and the power connector that plugs into the hard drive, if that doesn't solve anything then I suggest trying another hard drive in your machine and see how it performs.