When you get to the point where your partitions show up during the fresh install, delete and and all existing partitions and create a new one Ross. It will create a fresh system partitions. That should help.

I have some questions. I use Winstep and I keep four drawers. The reason I mention the draws is that when I clicked to open one all I got was a black background image. This happens occasionally where I'd get black background images behind an open window or app when it first starts up. Next question: What would make everything slow down to nearly a crawl? If I click anywhere on the desktop the wallpaper drops down a bit and is surrounded by a white strip. In the browser, didn't matter which one I used. It would freeze the I'd get a black background where the browser should be. I though maybe the graphics driver had something to do with it so I went into control panel and opened device manager. Right clicked on the Intel graphics and opened properties. I clicked update driver thinking that might be it. It found drivers and started the install. The progress bar stopped short of halfway and stayed that way for more than an hour. I clicked on the back button to see if anything was amiss then back to the download. It was searching for preinstalled drivers and then said the drivers are the correct ones. Now I'm beginning to wonder if the driver install caused all that. As for the damaged partitions I have no clue.

Always have to wonder about the basic "Is it getting hot on you?"  Is air moving through there, do you have any utility to check temperatures?

You might try pulling the Ram banks (2 of them I'm guessing) out one at a time to see if it works with one and not the other.  (You might need to have a specific slot filled when using only one.)

There's also the possibility you just happened to get a lemon new hard drive.  I imagine you don't have a dozen machines hanging around, but if you've got anything else to could plug the into to see if the drive itself works, that might be good.