I've read this thread from the start.
One thing I can tell without any doubt.
The harddisks themselves are not what's causing this.
Even the green Caviar running at 5400 should be more than enough to run any game.
What I would like to ask is a full list of all software installed on the system,
down to the smallest utility.
And a list with names and versions of important drivers
you installed, like chipset, audio, graphics, network card etc.
Also a more detailed description of the setup.
In your specs I only see external hard drives.
What kind of drive is the OS drive? Sata or IDE?
Are the games you have problems with, installed on an internal drive or external?
What frame rates and resolutions are you playing the games at?
In the BIOS have you set the disks to 32bit transfers?
Do you have a large amount of music or video files on any of the drives?
Although I ask for much info, keep the comments short.
Your first post was kind of hard to get through. Too much story, too little info.
I hope you know what I mean?