Is there a way to backup and restore everything *but* all the visible files?

Ladies and gentlemen, I have tried searching for various combos of backup, restore, system, environment, transfer, etc., with many hits but not relevant to this problem (I think): My boot drive is failing. I have backed up all the visible (and obvious hidden) files to an external drive. Is there any way to save everything EXCEPT the huge number of files I already copied? I'm guessing that means the registry, various system files, and maybe the MBR and stuff -- the stuff that will enable the new drive to be just like the old one? DETAILS BELOW

First:
HP m9715f about 3 years old
Windows 7 Pro, version 6.1 (Build 7600)

2013 configuration includes:
seagate bootdrive C 750GB from 2010
old WD drive (500?) with three partiitions
2TB exterior Seagate USB 3.0
2TB WD My Passport
I have Ghost 15.
I have a zillion emergency boot disks, including one made in the last day or so.

My boot drive is all one partition (which in retrospect looks like a big mistake)

One day Windows started working *really* slowly, i.e., right click on file, wait 20 minutes for dropdown to appear, click desired item from dropdown, wait another 20 minutes for selection to be executed. Many freezes (or being so slow that it appeared to a freeze). So: essentially unusable.

I tried rebooting, rolling back to various restore points (each of which failed as "corrupt file" or "couldn't find file"; eventually realized the C: drive was failing. After a day or two, it managed to reboot properly for some reason, giving me a big SMART warning about imminent drive failure. I tried Ghost and Window Bakup, but it would fail after a while. I therefore frantically drag-and-drop copied all my files to the external drive, came then compared total size of each directory, and hand copied whatever files (I guess mostly the huge ones) that hadn't been copied. This totalled roughly 450 GB, maybe a GB different from the C: drive total.

Then I tried every which way to make a complete backup with Ghost and with Windows. One way (I don't remember which) seemed to work, giving me 250-300 backup on one of the eternal drives. I took out the old C: drive, replaced it with a new Seagate 2TB drive. Tried to restore the big backup to the new drive; after about 12 hours it was maybe 20% done. For work reasons I had to halt it.

I later tried several times to start over, but I'd get various error messages and it would stop. It now seems impossible to do. I'm trying to convert my backup file to an image but that appears to be running even slower than the attempt to restore.

So I ask again: Is there any way to save everything on the old drive (to an external drive or a USB stick) EXCEPT the huge number of files I already copied? I'm guessing that means the registry, various system files, and maybe the MBR and stuff.

 

EFA11,unless I'm misunderstanding: As detailed above, I've tried that (albeit with Ghost and Windows backup, not with Paragon) and have an alleged backup. I have unsuccessfuly tried to restore. I have unscuccessfully tried to convert my alleged backup to an image file. For various reasons, also above, my real question is how to move the much much smaller elements that will preserve settings, WITHOUT recopying several hundred GB that I've already got backed up.

 

For one reason or another, every attempt to restore has failed. All but one attempt to back up has only made it all the way through. This all may be the result of the damage to the hard drive, but basically it seems pointless to do those procedures another time unless you mean that Paragon will be able to make it through where the other tries haven't.

 

The plot thickens...

I downloaded Paragon, and, yes, it seems to way better. For one thing, it allowed me to do exactly what I wanted above (I think): I was able to back up the MBR and hidden system stuff. I don't know whether that includes the registry (for instance), which I backed up separately with RegBak. I removed the old drive, installed the new one, and did a fresh Win 7 Pro installation. I'm waiting to see if that takes.

NOW FOR THE BAD NEWS...Currently the computer has only the new drive, the optical drive, and two external USB drives that have all the saved stuff. AND IT STILL HAS THE SAME SYMPTOMS, though not as terribly. I.e., Windows Explorer takes forever and also freezes frequently. Maybe the hard drive needed replacing, but there's clearly a second issue here that MUST be hardware-related, right?

The external drives are both USB 3.0. As before, each of them may or may not show up in the Computer folder and/or the drive/partition chart, often one place and not the other. Using the 3.0 adapter, they're almost never appearing.

Is their a history of 3.0 adapters being a mess? It's very possible that the first symptoms appeared right after I installed it, but I'm not at all sure. But I'm thinking: is WIin explorer (and other programs, like browsers) choking while trying to locate a bad 3.0 adapter?

 

Latest trauma: Okay: Ghost was able to restore the C: drive onto the new drive...I think. It took something like eight hours, and I was watching it on 99% done, but left the room. When I came back, the machine had shut down. Cool, I thought, it's done.

Then I turned it on: No beep, no signal, no nothin.

This had happened for a spell a few days ago in the middle of all this. The only thing I could think was some kind of hardware issue, so I unplugged my second internal hard drive, and everything was fine again (except for the original problem).

This time I tried it with only the new drive connected; then with only the old drive (the one I had been booting from when I made my backup); I tried both with just the red cable; then with each with the blue> (maybe green?). I tried booting off a bootable CD. I tried with a CD and NO hard drives attached.
Same result in all cases: no beep no post no signal. (The power light is on, the fan is going, the optical drive has light; whatever drive I have attached feels like it's on.) It happened immediately after the recover had (I think) completed; it's hard to believe that's just coincidence, but how could any software issue stop the bios screen? Particularly when I've tried to start it in all those ways.

Any guesses?