Wow, I don't think I've ever read a thread with so much bad information!
The 1 thing that a larger throttle body will do is increase the low end torque of the motor if the fuel system/ecm can deal with the extra flow. Low end torque being what is needed most in a 3.0!
No, the factory designs aren't perfect. Everything is a comprimise to something else. That is why companies like Jegs exist. The bad part is that the 3.0 needs to be almost completely redesigned to get any BIG gains. The bore and stroke of the 3.0 is capable of making MUCH more HP and TQ at lower rpms. Once again, it was built the way it was as a comprimise to something else.
If the cooling system is functioning properly, the installation of a 180deg thermo will keep the engine at 180 more often then any other temp. As a cold engine requires more fuel than a hot engine, the 180 deg thermo should cause you to burn MORE fuel and not do much else for you. The only way it should cause a gain is if the fuel map is closer to what it should be at 180deg than it is at 196deg. The engine SHOULD be more efficient at 196deg, doesn't mean it is.
Messing with things that the ecm controls is going to lead to a problem somewhere. Once you have done some mods, A custom ecm program would give much better results! Let me know if you find someone that will do that reasonable.
On a final note, I have 3 3.0 powered Rangers and I'm very happy with them. One I race offroad with good results. Gearing is the ultimate mod.