EFI is my preference... but then again carbs are pretty reliable too these days... The cost differences between carb and EFI are:
Carb, Manifold, and I think the distributor...
For EFI you will need a fox body mustang gas pedal, accelerator cable, EFI computer (The one from the donor car), computer mounting bracket, EFI computer wiring harness, injector harness, EGR Solenoid, O2 sensor harness, O2 bungs welded into the exhaust pipes or headers, Electric fuel pump, reworked fuel sender to accomodate a new return fuel line, inertia switch circuit to shut off the fuel pump in case of a collision. Since the engine is 12 years old, you will probably want to go through all of the sensors, and also cleanup all of the other engine hardware.. On the cooling system, I don't think EFI requires anything different than a carb engine would. The price seems high to me, but on the other hand the EFI setup does require a lot more hardware, and considerably more time to install. I'm not so sure on the AOD transmission, but I suspect it would be much like a T5 install where you would need a new driveshaft, and rear transmission cross member. The exhaust system would likely need to be reworked as well. Also, I've heard that the late model 5.0 headers do not fit between the early model shock towers, so you will likely need early model headers.
Then theres the 'what do I do with the air pump, and AC and power steering pump on the 5.0 motor.. relocating brackets, idler pulleys, or convert it from serpentine belt to standard v belt with a regular rotation water pump...
If 4-5K is in your budget, you might be better off buying a brand new crate motor and go with the carb, and a good working transmission.
I'm currently finishing up my EFI conversion. Considering I'm doing all the work myself, I don't mind throwing a little money at it... but now that I've written all this down, I can see why a professional installer would ask for several thousand dollars to do the upgrade... It is a lot of work, especially if you want it to look nice too!
Something you didn't mention is what engine is currently in the 66, if it's a 6 cylinder, you will need new engine mounts, front springs, and the cooling system upgrade, and exhaust system.. Are all these items factored in to the installation?