It shouldn't make too much difference as all the components will be grounded through a common component...the power supply! Well, in theory anyway However, for ease-of-mounting, if you're not going to be seeing the back side of the motherboard, I would take your (or any) old case, and cut out the motherboard mounting tray, and attach that to the plexi. You can cut this down to the size of the motherboard, and it gives you a nice, solid base, and will have all the motherboard mounts in the right place, which could be a PITA with plexi!
I would go for the Opus. As you said, the Carnetix requires the use of another DC-DC power supply, and only provides 60/80 W of power, more than a "standard" PC would probably use. The Opus is 150W, and will power even a Pentium 4 (there are people running 2.8GHz P4's from an Opus!), so the list of components you've specified should work well
The Opus is ATX, which is what your motherboard is
One thing I would check is whether your PC goes into Standby well..ie does it keep anything powered in Standby? If not, then I would set it up to use Standby once you have the Opus, my CarPC resumes to playing music within about 5 seconds of the power supply coming back on!