Seeming as quite a few of the "Related Questions" have answers by me, I am rather embarrassed to ask this, but I hope someone can help. I do have a solution to this problem, however, I would rather not proceed if I can help it.
A friend of a friend gave me a computer to repair that would not boot, I was told that they really want to keep their data but understand if I can't and "do whatever" to repair it.
My first thought before examination, based on talking with the person was hard drive (mechanical) failure.
I started by putting the hard drive in my copier and tried to take a backup (as I usually do for a first step). It succeeded.
I ran a few of my usual tools and they could not find any files or enumerate the hard drive at all. (I checked SMART data and did 2x full surface scans and found no errors what so ever)
Using a custom Windows PE image, I tried basically all the "normal" things, but as (I think) all of the Windows tools (excluding Diskpart) are file system level and not drive level, it was not at all successful. Diskpart was no help (I forget what it actually said).
I then used one of my favourite tools, Testdisk and was able to rebuild the partition table. (I actually mean rebuild, it became corrupt, it was not just deleted or other).
Now, Windows PE can go to the C drive, and I was able to see all the files - and "chkdsk /F" had a field day "fixing" things.
However, whenever I boot, I get the old message "A disk read error has occurred".
I have tried everything I can think of, I have rebuilt the MBR, replaced the bootloader (and options) but I am having no luck.
Also, I used Gparted and noticed a start and end blank block followed by a 5MB partition with an unknown format/partition. I deleted these and stretched the main drive to cover the entire drive.
Startup Repair does not work - it simply just suggests to remove any devices that are plugged in! It did this from the first time and only suggests something different if I use this option halfway through one of manual steps.( e.g. instead of deleting and then rebuilding the menu, if I do it after just deleting, it will automatically remake it - which isn't really any help).
My guess would be that whatever caused this error in the first place took out a boot/critical file, however I would of thought that Windows would boot and fail/bluescreen/other and not have this error. However, there is no repair install and SFC does not work from Windows PE. I am unaware of anything else that can do a file level scan and repair damaged files.
Anyway.... Time is limited I have been trying to fix this for the past 3 days (whilst doing other work... not non stop!), and just been going around in circles. I want to return this machine soon, so I will post the following as an answer if nothing gets suggested or if they do not work:
I have no idea what caused this error in the first place - I have done what the client really wanted and taken a backup of all their files, pictures and more. I am satisfied that the hard drive is not physically (or otherwise) damaged and partition tables do not just become corrupted, I think it must of been a virus and/or a random error. It is not know what else is effected, so I have performed a full format of the system and then copied back all the data back.
Edit- (Basically, this is what I did and it works fine - However, I don't like it getting the better of me and I copied the "broken" image back to the hard drive in order to try and fix it. If I can't come up with anything, I will just do this fix again - However, I am sure a repair must be possible.)