This is pretty much exactly what I've been working on for a little while, with a couple exceptions. So please let me know how it goes, and I'll post what I find when I build it (ordering the parts this week as soon as I finish negotiating pricing). As a site note, I've been talking to Howard at e-itx.com quite a bit and he's been very helpful as far as matching pricing and helping me find and build the right system. I'd recommend them to anyone out of all the places I've researched online.
VIA PX10000G
120G SATA
1G Dual pin Disk on Module
http://e-itx.com/apacer-adm-ii-1gb-fm1024a60c5g-tp.html
Note on this, the module plugs directly into the IDE pins with a female 44 pin connector on the reverse side, meaning you can plug the slot loading IDE dvd drive into the back. This saves a USB port.
Lilliput 2din in dash screen mount
PICO itx case (this is the only one i found, should fit entirely in the dash and eases cable management.
http://www.idotpc.com/TheStore/pc/vi...?idproduct=507
All of the other hardware is pretty much the same as yours as far as the power controller, USB devices, etc. The only difference is i'm taking the easy way out and using centrafuse. I'm a network engineer, not a software guy. If I tried to code in java i'd be the one guy out there that managed to make it explode. =)
That said ... if you get this working I would love to give it a shot. Always prefer linux over windows, and especially if its and open source FE.