I want you to do a couple of things fer me... and post the output here ...

First off get hdparm v5.2, it fixes some big issues with 4.6 (which is the "general" version in alot of Distros)

Compile, rename orig to HDparm, then install it.

Then: hdparm -i /dev/hda and post it.

Do a telinit 1 to bring you into single user mode.

Then: hdparm -Tt /dev/hda and post it.

Also I want to know the IDE chipset it was running with. Look in /proc/pci for that info.

Just FYI, I use this string for (most of )my HDs that are udma5 capable:

hdparm -X69 -d1 -u1 -c1 -m16 /dev/hda

Forcing everything to use PIO modes really make thing unstable... which is what you are currently running.