I have looked into this...
The first thing first is your cam dictates your firing order. The only real difference between the two motors is the roller cam and roller lifters.. Since you have a ** motor it runs the 351 cam, the ignition firing (spark plugs) order must be the same, so the ignition fire matches the valve timing.
I'm not up to date on an 88 bronco, but simple FI logic applies... SO if your original fuel injection system runs off of 1 oxygen sensor (1 O2 sensor before the cat). That means that your computer doesn't adjust the fuel rail by each bank (left or right side), it is adjusted by a whole fuel system and not divided (SO it's irrelevant in your computer's mind when the injector squirts). ** motors and regular 5.0 motors run the same injector, so matching the fuel injectors to the new firing order of the **, should get you firing on time.
Now i have heard by multiple sources, that keep the old FI firing order and run the ** 5.0 motor, it doesn't even miss.
But if i were to do the swap, i would reroute the FI harness to ** firing order, then you don't have to worry about it.
Hope that helps and good luck!