OK, I'm using this computer through the 'Disable Driver Signature Enforcement' option in the F8 menu, it's the only way I can use windows with keyboard and mouse, below is a small list of features where I can use the mouse and keyboard and where I can't use the mouse and keyboard.

Repair Computer = yes, full mouse and keyboard.
Bootlog = No mouse, no keyboard
Previous known Good Configuration = No mouse, No keyboard
Disable Driver Signature Enforcement = Full mouse and keyboard.
Start Windows Normally = No mouse, No keyboard.

I first booted windows into boot logging mode with no mouse and keyboard (luckily I previously set the power button to shutdown), then used the power button to clean shutdown, then rebooted using the boot CD and entered a command prompt, to which I issued:-

sfc /scannow /offboot=d:\ /offwindir=d:\windows

The rescue disk said D drive was the operating system, but under normal working conditions, C drive is the boot drive.

SFC found some corrupted files, but was unable to repair them, so I tried to use:-

dism /online /cleanup-image /restorehealth

But DISM threw and error at me so I can only use:-

dism /online /cleanup-image /scanhealth

DISM took a while, and wrote a log file, which according to the log, several files were replaced, but a normal reboot still had no mouse and keyboard, so I again booted into 'Disable Driver Signature Enforcement' option, which did allow me to use mouse and keyboard, I then used bcdedit to disable the driver signature check and to set test driver signature to on, which also made no difference at all.

So, I then booted into bootlog mode, which didn't have mouse or keyboard, waited for windows to fully load, then hit the power button to do a clean shut down, then booting int the 'Repair Computer' option and opening a command prompt, I read the ntbtlog.txt file and found 2 drivers were NOT being loaded.

Did not load driver \SystemRoot\system32\drivers\usbohci.sys
Did not load driver \SystemRoot\system32\drivers\usbehci.sys
Did not load driver \SystemRoot\system32\drivers\usbohci.sys
Did not load driver \SystemRoot\system32\drivers\usbehci.sys
Did not load driver \SystemRoot\system32\drivers\usbohci.sys
Did not load driver \SystemRoot\system32\drivers\usbohci.sys
Did not load driver \SystemRoot\system32\drivers\usbehci.sys

As can be seen, several attempts were made to load the 2 USB drivers, and failed, but they do get loaded when I boot using F8 ->Disable Driver Signature Enforcement

So, while in the command prompt, I copied over the 2 USB drivers from the startup disk drivers folder to the the boot drive drivers folder, and rebooted, and STILL no mouse or keyboard, it seems the signature enforcement is literally blocking ALL USB ports from operating, I found this out by trying different keyboards and mice into different USB ports, and still no mouse or keyboard, but then I thought "hang on I have some test equipment that can test USB ports", so I used it to test each and every USB port on the PC, and in a normal windows boot and windows fully loaded, there is no signals coming from or going to the USB ports, but when windows is loaded using the F8 -> Disable Driver Signature Enforcement' option, the USB ports are alive with signals, so this tells me that somewhere, windows driver signature enforcement is preventing all the ports from operating during a normal windows boot.

Any suggestions? Reformat and reinstall is NOT an option.