Let me start from the beginning.

My goal is to build a carputer with the features of a Kenwood DNX8120 (or DNX8140 now) for less money. Mainly I want GPS and iPhone integration - I want a unit that will drop the volume on my music (or video) to give me Navigation instructions or ring when my phone rings.

Here's what I have:
2.5" HDD (320gb WD Scorpio Blue)
Slim Internal DVD (Pioneer slot loader)

And here are a few pics of my progress.

My car - 05 MR2 Spyder. I found a post here by someone with the same car. He mounted his motherboard in the factory stereo. Thought I'd give it a shot.

JDM "Navpod" w/Lilliput eby701:

Stripped down OEM stereo:

Mockup - PSU mounted (*cough* glued *cough*) to the back of an original bracket, HDD sitting just below the DVD drive.

Looks good, right? But...
To make this work, I need to move the back of the DVD drive down.
To do that, I have to move the PSU down so that the back of the DVD drive (and the cables) will fit.
To do that, I have to move the PSU inwards so that it doesn't hit the rear connectors.
To do that, I have to toss the original bracket and build my own. It will hold the PSU, HDD, and DVD drive.
To do that, I need tools, equipment, and skills. <--- I'm stuck here, so I'm going to give up and buy a case instead.

I want a case that will house the m2-atx, motherboard, and dvd drive all in one box. I like the MoCoSo cases, so I'm probably going to do that

I'm having a tough time finding the what the trade off is with the Internal DVD/2x HDD version of the MoCoSo case, compared to their 4th gen case. Their blog says it has a "rearranged internal layout" but the extra space had to come from somewhere, right?

Does anyone have any comments on my hardware choices and compatibility with this case, or other case recommendations?

btw, I also am considering returning this motherboard if I cannot resolve the D945GCLF2 Shutdown Problem. I'll pick up a Zotac Ion D-E instead.