Really last question. If the BIOS has been updated since the pc was shipped do I still want to reset the CMOS as isn't that downgrading the BIOS?
I'm going to break the RAID and install the OS on a 3rd drive that isn't part of the current RAID configuration so that will eliminate any potential hardware issues with the RAID drives.
Resetting the CMOS isn't downgrading the BIOS. What resetting the CMOS does is clear any settings that may have been set on the BIOS, be it from your hands or someone else, back to factory defaults.
The reason that this is recommended, is that sometimes, people make changes based on what a configuration might be. However in some cases, some of those may not match up to ideal situations. Given I came late into this discussion, I cannot, for instance, be sure if you made modifications to the machine, like new hard drives, new video card or new ram. If this was a pre-built system, and normally, Dell does not tweak settings for when they build a system UNLESS you specifically asked them for a particular configuration, and most cases, that tweak would be for a RAID setup.
The 'random pausings' mentioned in your initial post suggests to me as some might have already hit upon, possible driver issues. I know that you should be able to find some Win 7/Vista x64 drivers for some of the hardware, given Dell does use some common chipsets, like Intel, nVidia, Creative and Broadcom for their mainboards, video, sound and networking. Your best bet is to try and identify the following if you can:
Chipset Type for the System Board
Chipset Type for the Network
Chipset type for the Video
Chipset type for the Audio.
Chipset type for the Drive controller
Chipset type for the Raid controller (If you have one)
You should then check on those devices, whether or not they are using the MS driver versions. In most cases, the 'twitchiness' I have seen is a resultant of the MS implementation of the drivers for those particular chipsets and will cause pauses like that as the MS baseline drivers are just there to get you going, but not tuned for performance, so will not function quite as nicely as the more up to date ones from the chipset manufacture (Although there has been the occasional WHOOPS from the manufacture drivers from time to time too.)