radiator problem: go to
http://www.radiator.com and buy a new lifetime warrantied radiator. yours will cost you $120 + shipping. its easy to replace doesn't take very long to do the whole dang thing. its like empty fluid, one electrical plug, 4 bolts, pull out fan, 6 bolts pull out old radiator. put in the new one, 6 bolts, put in fan, 4 bolts, one electrical plug, and refill.
as far as thermostat housing goes.
http://www.car-part.com try to find one there, if you can't find one there. go to a local salvage yard that has a 00-05 eclipse RS/GS and take a used one off. should cost you about 20 bucks or so.
now with the question as of who is right. who cares thats a awesome price for all the work they will have to do. most shops will quote 1000 or more for the same deal the dealership is offering to do for 400, and to offer to do what the other shop is for 774 bucks i'm surprised you don't live in Detroit. just make sure you only allow them to do the work for that price amount. do not let them pad the bill, i would also ask if you could watch some of the process being done. some shops will let their customers see what they are doing to your car. as long as you have safety goggles on.
water pump: what the mechanic said as far as labor is true. double if you do it later. i know when a water pump comes to mind your thinking big money to buy one. i just did a 30 minute check on google here is a brand new water pump for your car for only $32.95 + shipping of course.
http://www.google.com/product_url?q=http:/...&hl=en&sa=titlei don't think thats too far out of your wallets reach.
valve covers are just a pain in the ***, because digging all of the old gasket out is a *****! if you have a small dremel tool, (used mostly for arts and crafts) or know someone who does. i would get a tiny wood cutting wheel for it and you can dremel out the rest. since it is meant for wood you don't have to worry too much if it touches your valve cover metal, but still try to be cautious. a new valve cover gasket and spark plug tube seals cost 30 bucks from autozone. and for spark plugs get NGK iridium plugs they are known to last for over 100,000 miles. spark plug wires you will have to make your own if you want 8.5 MM as your car is a distributorless motor.
i think thats all the answers i can give you, i hope you get everything fixed.
sorry if this reply was too long, you had a lot of information to cover and i prefer to specifically answer each one. i hope this helps you as much as it can.