Help with system upgrade

The purpose of the machine matters. What do you do? Why have 2 GPUs? Why a Xeon?

I always start with the new motherboard and CPU first. But I haven't used a proprietary case since being completely bued by HP in the late 1990s. They use their own PSU coectors, which prevents commonly expected upgrades.
http://www.tomshardware.com/answers/...ocket-mod.html - yep. Proprietary PSU in that box.

I'd buy a standard case, standard PSU, new MB, and CPU. The performance on your current CPU is like a low-end desktop ($55 CPU). What is your budget for the initial parts? If you have $400, you are golden. You can save the cost of GPUs by getting an i5/i7 that have IGP onboard. If you aren't a FPS gammer, that would be fine.

OTOH, if the HDD is showing coection issues, check the logs, then that will need to be fixed. Sooner is better than later. Bad cable? Bad disk? Bad port? Swap each and see if it gets fixed. Might just be a loose cable too, so reseat it.