For thermal design a CPU is just a hot spot. I don't see Apple having a problem they can't handle here. A lot of cooling solutions can be found in the market already and I'm shure Apple's engineers know them all.
The test sites show a sort of "best case" for USB as there is normaly only one EHCI controller implemented which all USB2 connections have to share.Intel commited to build FW800 into their future chip sets only a week or two before Apple announced the CPU switch. Coincidentally
PCIe ATI 9650? Where did you find that?
ATI AGP cards are 9nnn. The PCIe cards are Xnnn or X1nnn. Only the X8nn got the Rialto bridge chip.
BTW a X1300 would be much better than the 9200 the mac mini has now, even the new ones with 64MB on a 128bit bus.