All sounds fairly standard to me, but:
Why spend the extra on an mini itx board and put it in an atx case?
May as well get a low powered (mobile?) amd and standard atx board. The difference in cost will help you buy a DC-DC power supply such as Opus or DSATX.
Also I wouldn't personally bother with padding either. The general consensus with base units is to mount them securely to something solid.
Next stop is software. Check out the Frontends section in the forum.
Best of luck.