The type of antifreeze should not have made any difference. Except for the so called "environmentally friendly" (propolene glycol) stuff, all anti-freeze is about 95% ethelyne glycol. The additive package is all that is different. Ethelyne glycol by itself is somewhat corrosive, and the additive package makes it more suitable. In spite of horror stories about incompatability, there really isn't any reason to worry about the different types getting mixed.
The color doesn't tell you anything. It's just dye. The fairly new Prestone "all makes all models" is green, but it's additive package is very nearly the same thing as orange DexCool.
The old Ford green stuff (also know as the "green snott of death") is high in silicate. The silicate falls out of solution after a while and leave behind a bunch of crud. It also allow the coolant to become acidic. Worn out "green snott of death" will cause cooling system problems of all sorts. Three years in the car is pushing your luck, and longer is certain to cause problems.
DexCool is GM's answer to overcoming the "green snot of death", but GM has had problems making a cooling system that works well with this superior fluid. DexCool as delevered in new GM cars and as sold by Texaco breaks down if fresh air is not kept out of the cooling system. Prestone's DexCool has slightly differnt chemistry and does not have the same sensitivity. DexCool uses OAT (organic acid technology) chemistry. This superior additive package permits the coolant to stay in the car much longer. DexCool is dyed orange.
Ford's answer to the "green snott of death" is G05. G05 is call a HOAT technology (hybrid organic acid technology). The additive package includes a very low level of silicate with OAT. This technology was perfected in europe and Mercedes has used it for years. Chrysler also uses it. Ford dyes it gold. Chrysler dyes it orange. Ford has published that G05 (Motorcraft Gold) is suitable for all Fords back to 99. Zerox (Valvoline) has published that G05 is a suitable replacement for the "green snott of death" in all cars. Valvoline has also challenged Prestone's "all makes all models". G05 purchased in a Zerox container is nearly clear, with a slight yellowish tint.
Back to your question. The type of antifreeze should not matter. All are good, even "green snott of death" if changed often enough. What could be bad though is if the coolant is "green snott of death" and is really old. If the coolant was not flushed with the water pump change you may be continually chasing cooling system problems, with the next weakest thing failing next.
And, yes, you could just have another bad water pump.
I would most certainly make sure that you do a thorough coolant flush when changing the water pump this next time.
Also check the belt tension, belt alignment, and so on.
