Hey there,
I doubt that your HDD has anything to do with your FPS drops since when it comes to gaming, most of the times the game loading times is the only thing that is dependent on the HDD (except when a game needs to load a huge amount of textures or some big file while in-game). It wouldn't hurt to check it, though. WD Data Lifeguard Diagnostic is a good tool to do that (here's a link: http://support.wdc.com/product/download.asp?groupid=810&lang=en) . Also you can run Windows CHKDSK /r to additionally check for any corrupted or bad sectors.
I've seen cases where non-genuine windows drops performance for a bit to check if it a legal copy or not and i takes some time to pop up the message and change the wallpaper to black. This might as well be the reason. I would suggest getting a legal copy of Windows with all the updates - this should fix any drops you currently have.
You can also do a run-in test from the BIOS to check the CPU, GPU and memory if they are working properly.
Hope this helps,
Captain_WD.