Well, there was an interesting (frustrating) turn of events...
The cloning process finished, and once I saw that it had only copied 502GB (there was about 840GB used on the old drive), I knew it wasn't going to work. I decided to try and boot it up anyway, but it just gives me a black screen saying the drive cannot be booted and gives a generic list of possible reasons. Being ok with that, as I had expected it wouldn't work, I decided to put in my windows 7 installation disk and just do a clean install - but when I try, it almost immediately cancels it and starts spewing pop-ups saying "X" file/folder is corrupt or unreadable, so the installation was cancelled. I also tried doing a repair install, and it did the same thing.
Did trying to clone the old HDD somehow corrupt the new one? Is there a way for me to format the disk and get it to a state where I would be able to run a clean install?
I almost had an anxiety attack when I started seeing the word "corrupted" in all those pop-ups.
S.O.S. Please send help lol
Use a GParted LiveCD (or the partition tool built in the Ubuntu LiveCD, which is probably GParted), and format the new drive. Or try and format it via the Windows installer media - though that's just a quick format and I don't suggest just doing quick formats. GParted will do a full format of the drive.