1989 F150 manual 4×4 wont go into 3rd and 4th gear

Before you go worrying about replacing the transmission at this point, I want to asked you, did you look at all of the gearing? Since about the late 1980s, most U.S. SUV equipped with manual transmissions also used synchronizers. Though most people don’t think this is true, it is, believe me. The synchros allow you to upshift and downshift without worrying about matching engine/transmission speeds manually so the gears won’t clash.

Think of synchros as something like a specialized clutch for each gear. Working automatically, the synchros allow you to shift smoothly and quickly and without much thought.

The synchros are my first suggestion. Next, I’d suggest having the transmission rails for third and fourth looked at. This should work so that when you shift into third, the gears lineup correctly and likewise with fourth. If the rails won’t match up then it is unlikely your transmission will shift as well.

Then, of course, there’s the shift pawl itself. Is it lining up correctly so that your Ford is going into the correct gear? How about the gearshift line? Is it binding in the carrier?

You started out your diagnosis work quite well, however, there is still more to go.