After reading this whole saga, Just had to make a few comments:
The JMicron is the slowest and buggiest part on an otherwise very good motherboard. It has been well documented to cause your kind of problems when hooking up to various hard disks. You should get the latest drivers from JMicron off the internet. The ones that came on the ASUS CD are known to be of poor quality. The latest drivers will fix most problems people have had using this part but it continues to be very dependent upon the hardware attached.
I would HIGHLY recommend you save whatever is of value off of those two old drives and then use them as paper weights. You have a nice top-of-the-line setup here and then you are compromising with old hard drives that have caused most of your problems and stress. If you really value what is on those old HDs, you want to save it now.
This motherboard was designed for SATA drives, not IDE. Get something like a new WD 320 GB SATA2 (7200 rpm plus 16 MB cache) for $90 plus shipping and plug it into the red SATA1 connector. The advantages are many including: much faster speed, higher reliability, sata health checking that warns you when the drive is about to fail, plus lower power needs (replacing 2 old HD with 1 new HD), and the new WD SATA will be very quiet.
NOTE: to use a sata drive in your system you need to setup as follows:
Backup the data on those old HDs. Then remove them and install the new WD Sata. Get latest Intel AHCI drivers for ICH7R south bridge from Intel's website. Load these to a floppy. On bootup of system, go into Bios, Main screen, IDE Configuration, set to "AHCI". save, and exit. Reboot system with Windows install disk and when it asks if you have drivers to install (option to hit F6) say yes and use the floppy. Make sure you load the proper driver since there are several on the floppy. You must scrol down off screen, not obvious, and get to the ICH7R AHCI driver. Continue with install as normal. It will ask for the floppy one more time after a reboot but that will be all.
I think you will also be able to speed up your boot time as well if you can then just disable the JMicro (after you install a new sata drive) plus if you don't use the MB fan connectors, disable them as well or at least the ones your are not using.
I would also recommend you get rid of the onboard wireless transmitter. Need to remove a screw on the underside of the MB, so it is a pain to get access. If you don't plan to use this feature, just remove it. No way to disable this within Bios, unfortunately.
One more caution, don't use the USB 3/4 connectors for anything you frequently disconnect or turn of/off. These 2 have special functionality for use with the remote control and some attached devices in these 2 ports cause unexpected on/off power to MB. You have 6 others so, avoiding these two shouldn't be a big problem.
Good Luck,
Paul