From time to time I don't have a Mouse Curser or Keyboard after Boot. Someone told me to set the Jumber from Master to Cable Select, which I did and I got both Functions back. Is this a Sign of a faulty HDD? It is 4 Years old and in the Power Options it was set to shut down after 15 Minutes. Should I set it to "Never"?

Are those USB or PS2 ?

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Cable select is for hard drives, not mouse/keyboard. Even if you wanted to use cable select, you need a special cable for that (it doesn't come standard). Perhaps when you dug into your computer, you "disturbed" something causing your mouse/keyboard to work?

A faulty hard drive will have a growing number of bad sectors (found in CHKDSK), or it will start making a clicking sound. It doesn't take control of your mouse and keyboard to let you know something is wrong ;-P The power options in bios usually specify inactivity time, so that it turns it off when it's not being used (to save power). It's not a timer that specifies how long the hard drive can run (otherwise your computer could only be used for 15 minutes before a reboot). If you leave your computer on for long extended periods of time doing nothing, then you can save some power and extend the life of your hard drive by setting a reasonable inactivity time.

I've heard of PS/2 ports dying before. Try a USB mouse and keyboard and see if that is better for you.