1) 16 GB of RAM? That's nice, but even with Windows 7 64-bit edition, the OS can handle more than 3GB, but each 32-bit appliaction (I'm not aware of any 64 bit ones that push statistical data yet) session is limited to 3GB max. So that might be a waste. you might want to re-evaluate this requirement
2) What? Clone means copy from one hard drive to another. Do you mean just pull the existing drive and install it in the new system? That will require a complete driver replacement for every single piece of hardware, in the OS. Not something to consider lightly, as it's fairly complicated. A repair install or OS reinstall might still be required.
3) A high-end processor ALONE could run you $300- $1000. Good luck on that one.
4) All motherboards can "optimize the IO speed". It's called "normal operation". As far as FSB goes, that was a LGA 775 socket feature, and is fixed (locked) to whatever CPU you get, unless you are talking about OVERCLOCKING which is a whole different topic. Besides the new Intel CPU's don't even have a FSB rating anymore.
5) Most graphics cards with 2 out ports can fulfill this requierment.
6) Power supply choice will be drived by his total power budget, which won't be that bad at all since he isn't getting a high-performance gaming video card.
7) Fans for what? The case? Does your case even have ports for more fans? What size? More information please.
8) As stated earlier, if going for "high performance", good luck on that budget.