Yep, this will be a fun project. Do you have the complete engine wiring harness with PCM as well or are you going for an aftermarket stand alone PCM? Also make sure the transmission will bolt up and that the crankshaft has a pilot bearing in it.
Engine Mounts: The 5.0 engine may require different mounts to fit correctly in the 2006 model's engine bay. Check if you need custom mounts or if there are ready-made solutions.
Transmission: Ensure the transmission is compatible with the 5.0 engine. You may need to upgrade or modify your transmission.
Wiring and ECU: A 2013 5.0 engine will have different wiring and control requirements. You'll likely need the ECU from a 2013 Mustang and potentially a custom wiring harness.
Exhaust System: The exhaust manifold or headers and the rest of the exhaust system may require modification.
Here are a series of video of the job being done to help as well:
https://www.youtube.com/results?search_query=Mustang+4.0+to+5.0+swap
If you have any questions while doing the job, please post images or short videos so we can help you along the way. Good luck on the adventure!
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Saturday, December 2nd, 2023 AT 11:25 AM