Here's my thoughts:
The X38 or X48 chipsets support full 16x on both PCIe slots (meant for Crossfire) so you won't lose any performance if you use the slot. Or you can go with a 780i chipset if you don't plan to ever use more than one radeon card. ~$200
It looks like the moncasos are the deepest HTPC cases at 18" compared to silverstone's 16.9-17.4". Maybe step up to the moncaso 972 or get a different case that has the dvd drive off-center? Maybe this one by Zalman: HD160Plus
or this other Silverstone: CW01B-R
BTW, I have a Moncaso 832. I assume the LCD problem you are referring to is the brightness of the backlight (too bright). It is too bright... but I personally don't mind it.