I thought I'd update this thread as I've been asked about this as well recently.
You do not need the two smaller PCBs in the X-51 setup, just grab the main board and you're good to go. You can simply treat it as a standard ATX board, everything goes in the same places.
Any new case's standard 2-pin power switch can be connected to the X-51 motherboard, the pins are below the SATA ports, in line with the PCI slot. The power switch, HDD LED, power LED etc. pins are also colour-coded just like your standard ATX boards. I haven't tested the LEDs yet since the X-51 has everything attached on-board, I just connected the power switch.
I built my X-51 R2 components over into a new case some time ago, the only problem I get is that the PC does not detect a power sensor on startup since power sensors are all on the X-51 case's internal PSU. The X-51 does have some built-in features that won't work on a new case, like the AlienFusion setup as well for example (depends on the new case, PSU and personal modification, really). Apart from that, it works just like a normal PC, with lots of ventilation and expansion space. I simply got a plain old Astrum GameDemon case for 20 quid, nothing fancy, and just grabbed a 550W PSU lying around in my apartment.
As for WIFI, just mount the antenna wires somewhere unobstructed in the case, I mounted them on the front of the case above the DVD drive, underneath the front cover and all works well.
Here's a quick diagram I made to show the basics: