If you're used to fast desktop computers (gaming rigs, high-end workstations, beefy servers, etc.), you'll hate the EPIA boards.
Shuttle does make motherboards and you can find some of the Shuttle units on ebay and whatnot.
My own project is a Shuttle case. Check it out here:
DarquePervert's Shuttle in 2003 Toyota Tacoma
If you want to lose the inverter, you need to keep the power draw of your system within the limits of the power supply you choose. With zootjeff's new DSATX pushing 220w, there's quite a bit of flexibility there.