A few comments:
1. When buying PC components I always try and buy the best (quality / capability) motherboards and power supplies. There are like an astronomer's mount - all other gear goes on them and if they're flakey - then nothing else will work well.
2. The HP Proliant micro servers seem to be making quite a name for themselves, mostly as home media servers. They are cheaper, more functional and just as expandable as a high quality NAS. When purchased probably best to combine them with Windows Home Server 2011 (no idea what that platform is like for astronomy gear).
3. If your USB ports are dropping out continually it gets incredibly frustrating. One thing you might consider is placing a high speed, powered USB3 hub between all your gear and your PC (meaning you may have to add a USB3 card to your PC, and run power to the hub).
http://www.netplus.com.au/product/CB...High-Speed-Hub or
http://cgi.ebay.com.au/ws/eBayISAPI....m=330622277895 A high speed, powered hub should be plenty fast enough for most needs at 5 Gb / sec and being powered it would run all your gear. It also means you only have to run one quality USB3 cable from the PC to the hub. I'm not sure what length active USB3 extension cables run in, but the alternative would be find a CAT 6 network cable to USB3 converter, run CAT 6 cable to the converter, run short USB3 from the convert to the hub, then run USB3 from the hub to your gear. This seems a nifty and extensible solution - so long as you can cheaply source all the gear. I'd search online first to see if someone has done all this with success first - as high USB is notorious for not working well on longer cable runs. 50 metres is nothing to CAT 6, whilst beyond 2 metres can confuse the heck out of USB2 cabling to devices! Additional some USB2 devices (e/g/ Meade DSI cameras) need special USB2 cables that deliver extra power to the device, a regular USB2 cable won't reliably work, you need the extra thick, extra wired USB2 cable they supply and then plug that into an active 5m extension cable with powered hub if you need to connect beyond 2 metres.
Hope these ideas help!