Make sure when you align your doors you leave then a little bit high in the back where the door striker plates are. You have to account for the added extra weight of all of the internals in the door and glass and such. I agree that you shouldn't install the front clip before you adjust the door. Do what you are doing. Work from stationary object "quarter panel" forward. Doors and then fenders. Tighten your core support bolts last. You may have to shift the front end over left or right to make the hood fit in the hole properly. Once the hood closes right then tight the core support bolts up.
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