If the 94 FI motors in good shape, it is an excellent option. Will bolt right in in place of the 289, and connect easily to your ax 15 transmission.
I did the same thing with a 95 motor many years ago.
One thing you will probably want to consider is buying Explorer front dress for the motor which is commonly available as a complete kit in the parts for sale section on this forum for not too much money. The Explorer front dress and mechanical fan are commonly considered to be amongst the best for cooling and EB with EFI. Also, if you get the Explorer front dress it comes with the harmonic balancer which is balanced correctly for the motor. You'll need to get a 50 Oz imbalance flywheel, available from WH and other vendors to go between the engine and transmission.
I bought the WH stainless steel braid fuel lines for EFI and their pump as well, but ended up using the lines only for soft connections and running hard lines which I bought at O'Reilly's along the frame rail. The WH kit is okay, but I wish that I had bought my own 3/8 (supply) and 5/16 (return) stainless flex with AN fittings (Amazon) instead of using the barbs and hose clamps supplied with the WH kit. You could also consider the Edelbrock 36031 EFI sump kit which would eliminate the return line, and also includes a fuel pump. Personally I opted for an EFI tank and ran the return lines. Internal pump tanks are generally considered to be superior, however I'm running an external pump mounted near the tank on the frame rail. Haven't had any issues so far and many people will attest that external pumps work fine and are easily trail replaceable without dropping the tank.
Another question is whether or not to use the Ford factory EFI or a more modern system like Edelbrock Proflo 4 which is what I chose. If you go with the factory system I have a Ron Francis harness which is still usable and mostly labeled, PM me and I'll sell it cheap.
If you go Ford EFI, keep the factory computer, and make an appointment with EFI guy to have it set up for your transmission and shift points. He can't remove anything related to emissions controls or give you more power due to legal issues.
The 3G/4G alternator is pretty easy to hook up to a Ford factory harness, and there are many diagrams here to help you do that, or you could go with a new harness from one of the aftermarket suppliers, again many debates about which harness is best here on the forums. I used Painless, although it's not perfect.
If you want to use your factory gauge cluster, keep or replace senders with OEM type, the oil pressure and water temperature sending units for the gauges. You will also need to install the EFI water temperature sending unit for the computer no matter what type of fuel injection you use. There are normally two bungs in the intake up front to make installing multiple water temperature sensors possible. Don't use a T fitting or neither sensor will get the correct temperature due to flow issues.
You're probably going to need a body lift and possibly bash in part of the firewall to clear the Mustang upper intake. Body lift is also helpful for the power steering pump/ resivoir with Explorer front dress. It's also helpful for your transmission conversion.
The Mustang EFI throttle cable is easily converted to the Bronco pedal by simply sliting the top of the accelerator pedal linkage at the pedal and turning it 90°.
Good luck with your conversion, this is an excellent path that you're going down.
JB