This should not be a problem as long as the wiring conversion is done properly.
The EEC has a electric shift enable wire.
For the electronic shift controller to make the leap to LOW RANGE the computer must tell it is's okay.
First by the truck must be in Neautral (Neautral safety sensor and circuit must be wired correct)
Then the truck must be stopped (speed sensor)
And the truck must already be in 4hi
Thats it, really its only one wire, it travels through the 3 pos clutch switch and also through the neautral safety wire in the tranny.
There are some slight differences in the wiring going to the tranny whether its a 5 speed or an auto, HOWEVER as long as the wiring is correct this should not be a problem.
(We had this problem when we did the 4.0L into Brett's 87 BII, because he used an A4LD and my truck was at the time the 5 speed, so we had to figure it out, simple wiring jumper at the clutch switch fixed it.....