Try the disk repair function of windows. It might take very long maybe even 24 hrs to complete. Either way things will get better or not, but if it is taking that long, it is likely that the HDD is the problem. The rest of your system specs are just fine. But a harddisk with lots of bad sectors, there is no cure for that, you should send the the drive back to your shop. Or install a spare one just to check it out.
I have had to send back a drive three times already because of spikes and audio stutter. Each time the shop returned me a refurbished one and the problem was gone (of course untill another one went bad 
)