1) The case is designed for miniITX motherboards. The one you've specified is microATX. It may not line up with the standoffs. Also, the motherboard is 24.5cm X 24.5cm. MiniITX boards are 17cm X 17cm. You've got a fitment problem.
2) The Zalman cooler is friggin huge. I seriously doubt that it will fit inside the Ampie case.
3) One thing you have not addressed is how you're going to power this beast. The CPU alone draws 89w on the 12v rail. There is no DC-DC power supply on the market that will push 7.5-8 amps on the 12v rail, which is what you'd need to power that sucker. That means you'll need a traditional AC-DC power suppy and an inverter. Inverters are more prone to inducing noise into your audio system, as well as horribly inefficient (they convert the car's DC power into AC, then the computer's PSU converts the AC back to DC for the computer to use).
4) What do you intend to use this beast for in your car? GPS navigation, playing MP3s and/or DVDs and/or MP4s, time-lampse recording wih a webcam, and just about any other vehicle functionality all running at the same time doens't need the CPU you've spec'ed.
In a very general sense, you need to do some rethinking of your plan for the reasons I've outlined above. I highly suggest you do some reading in the FAQ Emporium and some more planning to bring your system down to a far more reasonable level. One option you might consider is an Athlon64 mobile CPU. There are variations that will pull as little as 35w, but may not work witht he motherboard you've selected.