We are restoring a 68 coupe with a 200 6cyl. I want to put an AOD behind it. Anyone have any ideas which trans will work? I also have a 250 out of a 73 maverick, would this be a better motor to rebuild? I'm going for an every day driver and the best mileage i can get.  

If you want fuel economy, go with the 200 CID.  Less cubic inches, less fuel used.  The AOD would be an excellent choice for retro modding your classic with either the 200 or 250.

Back in 1972 I test drove new '72 Mavericks with both 250-6 cylinder and 302-2V V-8's and other than the sound when accelerating, there was not much difference in seat of the pants feel on acceleration.

Adding a modern transmission with overdrive is one of the best bang of bucks you can add to a classic Mustang.  With my 1970 Mach 1 with 351C-4V and modern T-5 five-speed I have gotten 25+ mpg on the highway.  When new, you were lucking to get 16 to 18 mpg.