I can't speak from experience on the AOD, but I can say that actually dropping the engine in will be a piece of cake. You just need a good set of 289 engine mounts. I will assume that all that is needed to fit the AOD is a new crossmember.
Hooking everything up is going to be another matter. The radiator will have to be changed or modified for the lower hose on the drivers side--again I am assuming you are going to run the engine with all the late model trimmings, like the serpentine belt. If you plan on using the old style pulley set, you will find that the harmonic damper has changed to four bolts. You will also have to use the old style water pump if you use the old pulleys--the new pumps are reverse rotation for the serpentine belts.
Wiring in the fuel injection is not that difficult. Ford even sells a booklet for about $5 that would really help. To me, trying to modify the fuel system is more difficult. A return line must be plumbed, and you have to use a high pressure pump. You might contact Windsor-Fox, they deal with this swap a great deal.
You will also need to have bungs in the exhaust for the oxygen sensors....which I believe are cast in to the stock cast iron manifolds for that engine, if you got the manifolds with it.
I am sure that I have overlooked several small details, such as the shock tower to cowl braces needing some modification to clear the EFI intake.....
I'm not sure of where the website is, but I recall some BRONCO site that had an excellent article on the conversion to the new engine. Take your time, and everything will eventually sort out.
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