Tuning for a 347 isn't a problem at all as long as you don't use a radical cam.
I wouldn't sweat using a GT40 intake on a 347 unless it's going to see crazy high rpm like constant dunes. Most Bronco builds are for low end torque and good road manners, following what the Mustang crowd does will just eat at the pocket book, shift the usable rpm range higher, and sacrifice idle quality. Bigger injectors isn't a bad idea if you're on an early 40 PSI system, if you go 99-01 the stock injectors should be fine at 65 PSI (unless you're running crazy high RPM).
The A9L is a Mustang computer, no need to hunt one of those down if you're using all Explorer electronics for the rest of it.
Valve springs should absolutely be upgraded if changing the cam.