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Should not be any 'Ford' parts at all if you did a proper install of the GM kit.
Straight out of the box it should run fine. Due to the internal bypass idle and low power runs (basically anytime you still have manifold vacuum) are exactly the same as stock - this means that the original injectors can work with the original tuning, you just won't be safe to boost it. Even with the 'proper' injectors you'll have trouble running boosted until the ECM gets re-flashed. Yes, the dealership will charge for this but you really have no choice!
Later you can play with different injectors and HPTuner if you want to explore real power. As it is now your engine should be running fine if all the parts are kosher and the tune is good.
Check your spark plugs for electrode burn. You installed colder plugs, right? Run too lean, too hot, too long and you'll fry that motor. Don't use fancy plugs...
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