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Swapping a 5.4 Modular engine into your Mustang's engine bay may require a few minor changes, mainly to the brake master cylinder. The booster assembly is too large to clear the longer deck height, so the valve covers run into the booster asembly/Master cylinder. Soome have gone to a HydraBoost set-up to maske more room. You may also need to relocate the Battery, Water Resivor Tank, and strut tower brace if installed. Hood clearance will most likely be a issue as well, depending on which intake system you use.
Other issues not presently thought of include fuel supply system modifications as well as oil cooler system problems. The radiator should also be up-graded to handle the extra heat.
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