bsiebert,
for the AOD you can read my write up on this as I have an AOD out of a Crown Vic in my truck. The Street Slammer Project Transmission

As for the pedal, it takes a little engineering. To old pedal goes through the the firewall and connects to a rod. When you step on the pedal it pivots and pulls the rod and the carb works.
The new pedal stays on the inside of the firewall and connects to a cable. When you step on the pedal it pivots and pulls the cable and the throttle body works.
So, you have to modify your existing pedal to work with a cable. I haven't found a pedal assembly from either a car or truck that bolts up to the same location as what is currently in the truck so the original will be modified. I found a picture on the web of one that someone else did but can't find it right now. Will post a link later.

You will also need to upgrade the alternator to a 3g setup. Not hard, but it is one-more-thing to do.

Sparky - it sounds like you have a plan but with all the prep work you are already over 2 days Routing the fuel lines should be done with the engine out if possible. It will make it easier. Where are you getting the lines from? Hopefully a truck since they will be routed correctly along the frame rails. Same goes for the main harness. I spent a lot of time leaning over the radiator and engine trying to reach the firewall to get things routed correctly.

All, make sure you install the fuel system inertia switch. This will cut off the fuel pump in the event of a hard crash or rollover. Mine is mounted on the back side of the dash.

Sparky - I mounted the computer in the glove box area. It just seemed to fit there. I have a center console on my bench seat so I don't really need the glove box anyway. As for the egr stuff, if you remove it you will need to get a egr eliminator (RJM Injection Tech » EGR Eliminators) so the computer will work correctly. Leave the egr mounting plate since this is where the throttle cable mounts and just block off the egr opening. You can buy a fancy block off plate for $15 ~ $20 or do like I did and take some 1.5 inch wide x 1/8 inch thick flat stock and make your own. 10 minutes and I was done.
Make sure the o2 sensors are hooked up. Mine aren't right now and the truck runs REAL rich and won't stay running since the computer isn't getting any feedback from the warm sensors. These will be installed this week. I am running long tube headers.

I think the battery mounts are different as well. I know for the Mustang harness the battery power and ground were on the drivers side whereas the '76 has the battery on the passenger side. Not a big deal to re-route, but it is one-more-thing to do

Have fun and go for it!