An update after a number of issues.
Come to find out that I have had to hard boot one to many times and damaged one of my new Seagate 2TB internal drives. For a long time it's been freezing. Tracking the issues in Console. Since pulling all my hair out, I have finally got a configuration that works for me. It may/may not other people.
After putting 1.08.2 on a "good" drive, I have the following configs:
System preferences:
Put hard disks to sleep whenever possible = UNCHECKED
Wake for Ethernet network Access = UNCHECKED
Allow power button... = UNCHECKED
Start up automaticallly after... = UNCHECKED
Computer Sleep = NEVER
Screensaver Start After = NEVER
I have my dual ASUS LCD display set up to a separate power strip from the computer and other peripherals. So - when not in use - I turn off the powerstrip and vice versa. So the Mac sees them as on - but they are not powered. I need access to my Mac all the time when I am not in the office - so it's natural for me to leave it on all the time. I just don't have a lot of processes going on.
Whenever possible - I only mount the external USB drives whenever I need them. Since I have internal bays - I use one of the internals for a back-up.
I've not had any crashes or freezes since. On a rare occasion - I put to sleep - but only if the USB drives are disconnected. I notice that if they are on - when in sleep of soemthing - it usally causes a wake issue.
Note- I have friends with other Mac systems, and they don't seem to have the smae problem.