What do you mean by designing your own case? While it's possible, it seems unnecessary in a fanless system.
You could always just use any second-hand ATX/microATX case without the power supply, and suspend/sandwich the HD's.
If space is at a premium, there are a few cheap options. If you want space for 2 hard drives, the Apex MI-008 is probably the best value option. $30 at newegg, but it seems to be sold out: http://www.newegg.com/Product/Product.a ... 6811154091
. It's a bit larger than you need (has a power supply you'll have to remove) but seems good value, just get a flexible PCI riser to use with it if you need to. There's a review of it here: http://www.silentpcreview.com/apex-mi008
There's a few posts here about the Morex M350, for which there's apparently a custom IO shield and PCI riser for the D945GSEJT, but I don't think you'll get more than one 3.5" HD in there.
Not really sure about controlling HD power. In theory, Windows power management can shut them down when they're inactive, but it's not something I'd rely upon. All I can really say is to make sure you turn off Indexing, etc to reduce wear on the SSD.
Finally, there seem to be rumours Intel is introducing a new low-power CPU and mini-ITX board in mid-January, apparently with the X4500 HD (1080p capable). Might be worth waiting for that.
EDIT: Had a closer look at the MI-008, don't think it actually needs a PCI riser. Also, the MI-100 seems to have the same specs, and only a slightly higher price (and is in stock).