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Stay away from the brand names that come to mind first... edge, banks ect for the 7.3s
Tony Wildman, Beans Diesel Performance, TS chips, Swamps Diesel, all those will make you a chip that will work alot better for you then what edge products will do for you.
For fuel economy, it doesn't matter much, so long as everything is working properly... I know my manual hub 4x4's get comparable gas mileage to similarly equipped 4x2's.
If you plan on towing alot, i mean 3 times a week then get a stanard. If you plan on modding it to go fast go automatic. There both good transmissions. The ZF5 you will hear alot more of the truck driving. Its noisy.