Slow, freeze up

My system is running super slow. Even when I am running a hardware diagnostics on the hard drive the system takes over 24 hours to run. When I try to do a boot and nuke, quick method it takes over 12 hours to run. When I tried to do an operating system restore, it takes for ever and some times it freezes up. I am not sure if it is a problem with the harddrive or the computer itself. The fan seems to be running normal, ie it runs fast when first turned on then slows down after 10 seconds. I even tried taking it apart to clean the fan, still there is no change... I put new heat sink grease on the CPU but left the junk that was on the north chip? could it be the northchip is heating up and giving problems? I should have cleaned the gunk of the northchip, and dont really want to go through the process of stripping down the laptop and reapplying heatsink grease if that is not going to solve the problem. When I ran hardware diagnostics, the CPU and mobo tests fine. But the system is running much slower than normal. This system has a dual core CPU so it should be running fast