The downsides to doing EFI will be, some additional electrical work, and tuning, whereas, a carburetor, you can tune yourself, without any expensive software. And you can use a HEI distributor, which are very easy to learn to tune.
Swapping an existing fuel injection system from a car such as a Fox Mustang isn't to difficult but there is definitely more involved with it (Electrical, fuel system, etc.) than doing a carbed-engine swap.
What kind of EFI system are you thinking about?