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Well parts maybe 1000 that leaves 4500 for labor sounds a little high to me but i'am no expert, maybe somebody that knows a little more will chime in and give some input.
i had new oil cooler , egr delete, arp's, ford head gaskets , blue spring update , coolant flush and new fuel and oil filters and oil all for about 3400 including parts, i purchased all of the parts myself and the tech at the dealership did it for me on the weekend.. i live in nc
3500 is not unheard of. That really is probably closer to average. If the shop will let you buy the parts it will save you a lot of money. See how much there labor is and go from there.