No, I didn't know about the hard drive needing a cover, seems like it would get hot.
If you lived in San diego, I would come fix your computer. I most likely could figure it out.
To see which new program you have: Click the start menu, settings, control panel, double click add or remove programs and look and see which new program is there.
As far as the new found hardware, it is probably something like a usb hub, or a mouse, or a printer, that got upset when things were unplugged and plugged back in. You may have to uninstall a program and re-install it.