Agreed on both points. It would likely have been simpler to update the 2.9, especially since all the leg work to fix it's major issues had been done on the 4.0. It was largely just a matter of updating some of the procedures used in producing the block, using different lifters, and re-writing the 4.0's software to use the 2.9's air/fuel tables. It would have been a simple matter to change the 2.9 to EDIS and put the EGR back on, which likely would have been enough to make the emissions up to snuff.
As for needing three engines, that is a common trope of Ford trucks, you usually have one small engine with a low cylinder count, and then two larger ones. I agree the 3.0 should never have been considered for the Ranger. It is fine in a car, but in the Ranger it tended to roughly match the 4.0 for fuel economy and the 2.3 for power.
As for the people who decided to use it, well they were very highly educated. And if they had actually been smart they wouldn't have needed to be taught so much.