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Dual-core 6 GHz processor

Wow

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650 watt power supply

If you're ever going to run ludicrous resolution (its all plaid) with two video cards linked together then you might want to get a beefier power supply.

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3) I'll be running 32-bit Vista for the operating system (I have a lot of legacy software and I want to maximise my chances of compatibility, so no 64-bit for now although the hardware will be 64-bit compatible). What "gotchas" should I be on the alert for?

Vista and compatibility is an oxymoron. If you want more compatibility then run XP. If you need even more than run Windows 98...

Tell the engineer to not activate Vista. Leave it unactivated and before the 30 day countdown expires, do the rearm trick. You can do this a maximum of 3 times. When you can no longer do it, then you actually activate Vista. You'll then have 120 days to fiddle, tweak and reinstall the system with no worry about having to phone up Microsoft to reactivate it.

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I have kept the original files of all downloaded programs like AVG and Emplode and Exact Audio Copy and FireFox and Google Earth and Hyperterminal and ICQ and Lame and MP3TS and Spyware Doctor and Total Recorder and Trillian and Tweakui and Winamp and Windows Media Player and Winzip and ZDOOM

As Dignan said, you will want to get the latest versions of all of these. TweakUI hasn't been released for Vista and running older versions isn't recommended.