OK so meerly the presence of the RAID drives connected in the system even if they aren't being used to boot from could impact performance. Sorry I didn't understand that and didnt have a USB hard drive. I tried to put it on my pc but could not make the backup work without errors. I'll disconnect the RAID and get a USB drive as you suggest. For what it's worth so far the system is running fine with the RAID attached, but sonds like not helping the cause.
I was being a chicken with not formatting the RAID (i.e. keeping the old setup as a backup) as had a spare drive to try out the new OS. I thought once the new OS was running consistently I could go back and break the RAID etc.
I have made extensive notes of every step taken with the current OS install.
Note - You could also try and image the RAID to an external hard drive as well if you wished to preserve the data.
Another thing to note, whenever you are dealing with something that affects performance, in this case, the RAID itself, you may have to use the manufacturer drivers, as I mentioned before. When the system has to access or do something that involves hardware and you see a plummet in performance, this is a key indication that whatever hardware being accessed may not be accessed in the most optimal way.
For others - Things that slow down the computer will be one of a few things:
1) Disk Access - The slowest part of any computer will be the Hard Disks themselves. If the disk is suffering problems, it will DEFINITELY slow the system down to a crawl, especially if it has to access something from it.
2) CPU Usage - Next to Disk Access getting killed, CPU usage, as processes take up more CPU time, other processes are waiting behind that one for its turn. If you see your system capping out processing wise, the slower it will go.
3) Memory in general - Low Memory with high memory usage, evidenced by low available memory (And I mean AVAILABLE, not Free) and really large memory paging - Which invariably leads to higher disk accessing for Virtual Memory (Which might only happen at the 32 bit level and lots of programs going)
Now, I maybe recalling incorrectly, but Windows does occasionally poll the drives. RAID drives do get the occasional poke to insure consistency as well as status. Depending on how a person sets up their system, or where they start putting items, disk access can vary over time. Large transfers to a disk array will often times require a bit more 'assistance' than just the baseline drivers, mostly with Hardware RAIDs due to how the RAID controller handles data. If you were using a Software RAID architecture, the problem would be less about the OS being able to talk to the drives and more on the OS, Processor(s) and software handling the RAID information.