Random Gain of 9-10 Gigabytes, Want to Know if Assumptions Correct

I have a 320 GB hard-drive with several bad sectors that I was going to repair with HDD Regenerator, but I heard that it sometimes has bad results so I decided to clone the drive before using it. Unfortunately, Clonezilla failed and managed to damage an unknown amount of files on the drive shortly after starting the cloning process. Windows stopped starting up properly, not recognizing my account's administrator status and not loading any programs at all upon login, including explorer.exe. After several failed attempts at fixing the drive with Chkdsk and Startup Repair, I finally decided to re-install Windows on another hard-drive.

However after I re-installed, I noticed that the free space on the older drive had suddenly increased from about 44 GB to about 53 GB. In checking my personal files it seems the majority of them are there. However, the Windows folder on that drive is only 14 GB. Coupled with the bugs I experienced, and the fact that the minimum hard-drive space needed for W7 64-bit is 20 GB, my theory is that at least 6 GB of original W7 system files disappeared, while an additional 3 GB from System Restore points, various programs integrated into the system like C++ Redistributable and .NET Framework, Updates, the WinSXS folder, temporary/miscellaneous files (though probably few since I use C-Cleaner often) and etc. were lost as well.

Is this plausible based on what I've described? I haven't gone into the system folders often and I'm not sure if what I'm saying makes sense.

Unless you had "before" file pictures of the bad drive, you can't tell.
My Win 7 64-bit "Windows" folder is 15.2gb, so your 20gb assumption is wrong.
That folder size can widely vary, for example by running cleanup of service packs.
Speculating about undocumented files sizes won't get you anywhere.
But it can be fun digging in and learning about it, so I encourage that. You appear to be curious enough to get into that.
Make sure you make system imaging a habit if you do get into making system changes and experimenting. That removes all the danger, provides previous pictures of what you had, etc. It's a real good habit even if you don't experiment.
Would have saved you the problems you ran into with cloning.

How long have you had Windows on your computer? With my fresh install my Windows folder was about your size, and I feel that 14.5 GB is abnormal for a system that had been used for three years with all updates installed.

What is system imaging and how do you do it?

Additional questions from another forum I posted this on:

The thing is HDD Regenerator only marked 486 MB as bad, so I'm not entirely sure how 10 GB disappeared. I haven't checked in detail, but do you guys think that it's likely that the majority of lost data was from the Windows folder? I'd been using that drive for 3+ years at that point, though I usually cleared temp files using C-Cleaner and never went into hibernation.

Both HD Tune and HDD Regenerator found the bad sectors early on in their scans, and since I was having slow start-ups I figured the files that were stored there were system files. Since Clonezilla failed so early on, is it likely that most of my personal files were not damaged?

Also SeaTools began detecting errors around sector 6221840, I figure that would be around 6 MB in, and I'm not sure but are harddrive sectors arranged from oldest to newest? If they are than it's even more possible that mainly system files were lost.

I've had this Win 7 almost 3 years. It has SP1, but I did a cleanup after installing that, and got back 3-4 gb. I have most the critical updates up until a few months ago.
Can't answer questions about HD sectors. I just toss a hard drive as soon as it has a mechanical problem. The magnets are good for finding drywall screws/nails.
If the old drive is still readable, I suggest using a "tree size" utility to narrow the differences in old vs new drives if you pursue that.
Here's a tutorial on imaging.
Imaging with free Macrium[2]=Backup Restore
There's plenty on this forum about imaging, and many willing to answer questions.

What clean-up tools do you use?

My old drive is still readable, and the majority of my personal files are still accessible. I'm not quite sure if it is a mechanical problem; the whole thing started a month ago when the computer came back from standby and was frozen. I'm guessing the tree size utility can't find changes in hard drive data unless it's analysed the drive before though, right?

It can only read what the drive is capable of reading. You would have to compare what it sees to your working system, since you don't have an original picture.
But it quickly reveals wide directory size differences so you can drill down.
You may be able to more quickly find missing files on that old drive. Especially obvious would be missing files you determine are necessary for Win 7 to work properly.
I think I said you'll never find all that got hammered by the failing drive, and I wouldn't bother doing it myself. But it might satisfy your curiosity.
Personally, I only care about Win files when I want to streamline the system for imaging. If I have any problem with Win, I just restore an image.
It's really simple to image. The tutorial I linked has to provide a lot of detail because that's the nature of a tutorial.
To cut to the chase, if you download the WinPE Macrium ISO file whs has generously provided, burn it to a CD/DVD, and have a spare drive, you can be practicing imaging in half an hour.
After another half hour of practice, you can be restoring Win 7 in 5 minutes, and never have to reinstall it again.

So I installed TreeSize Free to analyse my drives. Seems I was mistaken earlier on about my Windows folder.

I found that the System Volume Information folder on the old drive seems to be empty in comparison to my new one, but my new one only seems to be half a gig. Also, I can only see it with special options turned on, and it didn't factor into the used space in properties until I turned those options on. Do you think the loss/corruption of files in that folder had an adverse effect on proper reporting of hard-drive space? Also, could you check the size of your folder in comparison (because I'm not sure how much that folder changes over the course of 3 years; it would also be helpful if you could check the size of your Recovery, Documents and Settings, and PerfLogs folders as well).

EDIT: I just realized something strange: TreeSize Free reports that a fresh install of Windows on the new drive takes up 19 GB, but disk usage in properties reports that only 14.5 GB is taken up. However, if I select all folders including hidden system ones on the drive, I only get 11.0 GB. I would have to include either the page file or the hibernation file to get the number that is reported in properties. So my question is, what exactly does Windows choose to include/omit in that calculation?

Have you run a System File Check to see if you have any errors that can be fixed?

SFC /SCANNOW Command - System File Checker

It sounds like you have a lot more system problems than just the free space issue.
When you installed Windows on the new HD was that the ONLY HD connected?
If the old HD was connected during the install to the new HD that can cause problems.

I would re-install windows on the new HD with ONLY that HD connected.
Take a look at this tutorial by gregrocker.
Clean Reinstall - Factory OEM Windows 7