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Try bleeding the air out of your cooling system. Thes engine are notorious for doing what you just described if the air bubbles aren't bleed out. Park it on a angle with the radiator being the highest part in you engine compartment. Turn your heater on full blast and let it idle. Remove the radiator cap while it is idling and let it sit until it runs normal, adding coolant when needed. Then put the radiator cap back on and drive it around. This should fix it. It has something to do with the bubbles going by the water temp sensor for the computer and causes it to go rich, then lean, then rich, then lean.... I've seen this alot at the dealer after doing a bunch of engine work. It still might be something electrical because this was a swap, but check the easy stuff first.
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