Just thought I'd post this in case any other istoryans find themselves in a similar situation:
Intermittent problem with the following symptoms......
System hangs.
Slow Boot-up.
Failure to detect drives.
Interrupted audio/video playback.
Sudden restart.
Check Event Log for critical errors, specifically
Atapi Error 11. Do you see lots of these?
If so the problem could be your mobo's SATA controllers. Here's the good news... you don't need to buy a new mobo as you can buy a PCIe controller which will just plug in. Kind of rare in PH, but you can order online from China for a few dollars. A cheap and effective solution to an irritating problem which took ages to diagnose.
Here's another tip... SATA cables and connectors are basically poorly designed and if you swap drives around often you will inevitably shorten the lives of both.