fix_hdc should work: http://www.911cd.net/forums/index.php?showtopic=20464 I think it's in ubcd4win, which might be easier than building your own bartpe and maybe integrating mass storage drivers: http://www.ubcd4win.com/
Eh? Raid 5 copes with the loss of a single disk, and the data remains available for read/write, just at increased risk. If the raid card can't rebuild the array while it's up, it's not a very good one.
What are the IP addresses and netmasks? If B is doing NAT but C has a routable address then you might be able to connect to it, but if A is doing NAT then you're probably out of luck...
If you don't have a win pe / bartpe disk, you could try autoruns and process explorer - some malware prevents these running based on their filename, so try renaming them if they fail to launch. Good luck!
It depends on how clever your nat router is - some will know to open related ports, but with consumer grade kit you usually have to open ports for torrents and xbox etc, if not using uPnP. Please do link to the win8 pdf - I'd like to know what /GS is. Cheers
There could be wake-on-lan options in the network card driver, or in the bios. Sometimes they get creative with the descriptions, like PME (Power Management Events) or "deep sleep". Or there is always the wall switch...
How would link aggregation help? If you have managed switches then you could look at the error rates, otherwise I'd try to isolate which switches / host nics / cables are involved, and try replacing them.