SOLVED (kind of!):
First of, thank you everyone for your bountious help. I have run my system for a few days to make sure the results are accurate.
I did this:
1a) Unpluged second HD. Imediately no more NTFS errors at boot.
1b) Complete format of main HD.
1c) Installed Windows (MCE 2005, basicaly XP with service pack 2).
2) Then installed Nvidia 6.39 (minus IDE drivers and firewall/Active Armour - just said 'no' during install).
3) Then installed nvidia 66.93 official (sorry FastEddie, still a newb).
4) Then Marvell Yukon driver (enables 2nd internet plug).
5) ZA 5 firewall.
6) Kaspersky AV (I was still getting KLIF errors, so I upgraded my KAV, and install was clean - original problem could have been KAV version).
7) Windows updates from web.
8) Connected second HD. Recognized.
All went well and smooth. I heard ZA 5 has a lot of issues, especialy with bittorrent, but I have't noticed any. I was unsure about sound drivers though - do we install both Nvidia and Realtek? Sound was working after step 3, but it sounded a bit flat though (could have been my imagination), so I installed Realtek a few days later. Now there is a conflict and the Nvidia mixer won't open due to "driver conflict". Also (may be my imagination again) but the disk read/write seems a bit slower than before.
What cha think?
Any more word on the stability of the IDE drivers, NCQ, or nvidia FW/controlers? Can I try to upgrade, or must I reformat again to do that?