So… here’s my input…
@sgtsandman is correct, improper cleaning out of casting sand was a big problem.
@PetroleumJunkie412 noted that and also noted that the European market didn’t have the overheating and head issues that we have with the 2.9, so I’m going to say there was poor quality control here that caused a lot of problems. Throw in poor maintenance and general abuse and it’s no wonder there were so many problems and a bad rep.
Sediment in the cooling system from lack of or improper maintenance is another problem. My first Bronco II, I wanted to flush the radiator and when I opened the drain plug. Well, nothing came out. Unscrewed it completely and still nothing. Poked around in the holes and hit it with the hose a few times and finally got the tiniest drip. Ended up pulling the upper and lower hose and going to town spraying water in everywhere. After generous water useage, water would come out the drain hole. Hosed out the heater core and block as best I could, filled it with coolant flush, ran it, drained, sprayed, filled with water, ran, drained, sprayed, more flush, ran, drained, sprayed, water fill, ran, drained, sprayed, water fill, ran, drained, sprayed and finally wasn’t getting any more junk out. Then the motor ate a valve.
My choptop had been overheated by the previous owner when I got it and cracked a head. I chased the overheating problem for awhile and broke a couple more heads. Turns out a substantial part of my woes was a result of a leaky heater core and someone sealing the heater core box with RTV. Looking back, I’m also suspecting an issue with the block being choked up with casting sand. It might be buried in my shed still. The 2.9 that went in the last time I broke heads never gave a bit of trouble. I flushed it and ran a new water pump with a 180* thermostat and a 4.0 radiator. With a manual transmission, 4.10 gears and 33’s, it ran great and was a solid 18/19 mph around town and low to mid 20’s highway, so I have my doubts that there was any negative effects to my cooling alterations. It didn’t like 35’s though, so it got replaced with a 4.0. Well, a few of them. Haven’t had much luck with those motors either in that.
One thing to note, factory spec for thermostats for the 2.9 was 192*, however most “stock” replacements for it are 195*. I don’t know if there is a 185* or 190* thermostat available for these, but I would definitely be a little more comfortable running slightly colder than slightly hotter.
Overkill on the cooling system is possible. My F-150 is a prime example. Even with a new radiator, water pump, and a flushed cooling system in the winter, it wanted to overheat with the plow on. 180* thermostat, super-wetter and a 50/50 or 40/60 mix of antifreeze/water and tilting the radiator slightly back at the top solved that problem. But without the plow on it runs cold. Even in the summer working it hard.