ALL-IN-WONDER X800 GT 267 and Intel HD i5-2400 304 So the i5 seems to be "better". But both are not usable for gaming. You should use at least a Radeon HD 5(6)770 for gaming. But better start with a HD 6870, this card is fast enough for MW3 and BF3.
this will never happen. If you want to use new hardware use a new Operating system. If you don't like Windows NT based version go to Linux (Ubuntu for expample).
which GPU do you have? Some users had issues when the GPU shares the IRQ with other components. So run "C:\Windows\System32\msinfo32.exe" and check under IRQs if the GPU shares an IRQ. If this happens and your board has 2 PCIe 16 slots insert the card in the other slot and test again. If this doesn't help, compress and upload the trace to mediafire.com and post a link here.
NDIS causes 1 spike over 1000µs: The L1C62x64.sys is your network card driver for your Atheros L1c PCI-E Gigabit Ethernet Controller. I can see that this driver causes some CPU uaage spikes of the SYSTEM (Kernel). Your version is 1.0.0.26. Check if you can get an driver update. Also install the Windows 7 Sp1, you still use Windows 7 RTM. Do you need the software VAIO Care? This tool captures data every 2 seconds and may cause this spikes:
SMART = Self-Monitoring, Analysis and Reporting Technology: http://en.wikipedia.org/wiki/S.M.A.R.T. There are several tools which can read the data (Speedfan, HDTune, AIDA64).