It may or may not be the pilot bearing. Pilot bearings usually make themselves known by difficult shifting, particularly into first or reverse while sitting still. Are you sure it only makes noise when actually trying to engage the next gear or does the noise start when you push in the clutch pedal. If the latter more likely the throwout bearing. If it's not the throwout bearing, and it's not difficult to shift , it may be an internal input shaft bearing. in my experience a throwout bearing will make noise for a looong time before utter failure. A pilot bearing will annoy you with difficult shifting and an internal bearing will complain and fail slowly. I'd let it develop unless you are a full timer, then you might want to pick your time and place for repair rather than leave it to chance. If you are on a trip and returning home in the near future my thoughts would be finish the trip and don't flog it. This is a good question to take to a Ford truck enthusiast forum as they will have people that have exploded these trannies and a lot more experience fixing them.
Bill