I adapted a build I suggested in another thread, this should be good (probably even overkill on the GPU) for you.
Have the HDD's in RAID1 and that gives you your disk failure protection, though it means that you have 2x1TB drives for an effective 1TB of storage. Backing up to an external drive is always going to be the best solution, if annoying.
Future upgrades, really depends what your going to be doing. For now, its a good gaming rig and a decent workhorse.
Theirs nothing in particular that would hold you back from upgrades other than not being able to Crossfire/SLI on that board and PSU and maybe custom water because of the relatively small case.
Probably partitioning the SSD and installing Linux on that partition. Have it set to boot to Windows by default, and when you want Linux, hit whatever key (for me its F11) during the mobo splash screen to bring up the boot menu, from there you can go Linux.
At least thats how I would do it.