Bit of an update.
Just for giggles I bought a TIM kit and reapplied the thermal paste as well as putting a new motherboard battery in.
On booting up Windows tried to install various bits and pieces but didn't say what they were - for about an hour it flashed up small boxes which said Windows is preparing to install files. However, the messages were all the same and only flashed up for about 2-3 seconds each during this period.
It then tried to install Ad-aware for some reason but kept failing each time as there were no files to install from. It was as if Windows was trying to repair Ad-aware as it wasn't opening up a Lavasoft programme.
I managed to cancel the Ad-aware installation box which failed five times. I couldn't remove the various Ad-aware files which were dotted around my computer as the there was "an installation in progress". In the end I had to re-download it then install it and then uninstall it.
HOWEVER, I ran Malbytes again and this time round it found a Trojan and something else which contained reference to Ad-aware...
Managed to get it removed and after several scans I'm apparently clear now. However, the machine is still struggling with simple tasks. I tried to install AVG but the PC just gave up.
Any suggestions would be greatly appreciated!