I just did that on my '94 4.0l 4x4 yesterday, went pretty smooth.
The main thing is not to load up the auto hubs with grease, wheel bearings yes, but keep it out of the front area.
Light coat is all that is needed on the plastic auto engage sliders.
It reads like one or both the auto hubs are not disengaging fully, which is why I mentioned the above.
You can try putting it into 4H then drive forward 100ft, the back to 2H and back up 75ft to disengage auto hubs, see if clicking goes away.
Although this type of clicking shouldn't come and go with the brakes.
That almost sounds like the calipers are loose