In looking at your specs I think your storage is going to be the hardest to deal with. Todays 1TB drives are quite fragile. Drop them from a table and 90% of the time they are goners. In addition without serious cooling they can get very hot (I am looking at you segate) and once you get upwards of 55 Celsius they start to break down fast. Even worse would the temperature cycling due to the fact the server is not online 24/7. Seeing as you are power constrained its probably not going to feasible to go with a ton of 250GB drives ect...
To build something like this in a ruggedized form is going to be expensive (5k + for the basics) Is there a way you could reduce your data requirments? 4TB is a tremendous amount of data.
If you were willing to compromise
One other suggestion. Go with a MiniITX board and a DC-DC power supply
This one is cheap and you could put an AMD CPU in it
http://www.newegg.com/Product/Product.aspx?Item=N82E16813500021
Then add a 45 Watt AMD CPU and maybe RAID 5 with 500GB laptop HD's
In theory you could build a decent dual core 2.6 Ghz system with 1.5 TB of storage, 4GB of ram and all powered by 12Volt DC (negating the UPS need.. just use 12volt Batteries) for a reasonable price. A system like this would be small and portable. If you needed more horsepower I would suggest building multiples.
It would likely be much more cost effective to build multiple moderately powerful systems than one massive one.
