Q: 2003 lincoln navigator motor 5.4 does fit in a 2003 ford expedition 4.6?

The hardware and software of the computer (powertrain control module) and transmission control module (TCM) in the Expedition will only work with your present 4.6 L engine. If you change the stock engine to one that is not a catalog interchange for the car (the Lincoln 5.4 L engine does not interchange and is not even the same engine as the optional 5.4 L that was offered as an option on the Expedition) you will have to carry over the "new" engine’s computer, TCM and complete vehicle wiring harness in order to get the new engine to even start, let alone run. Adding to the complexity, if you install a larger engine, that typically increases the weight in the front of the vehicle which means that you will have to re-design the suspension of the vehicle. Unfortunately, with modern cars, there is no practical possibility for using non interchange engines unless your intent is to completely re-design the vehicle. If your engine has failed, and thus you simply need a replacement used engine, please note that you will easily find many direct drop in interchanges using on-line used parts databases such as Car-Part.com. Finally, if you are interested in an engine replacement (OEM to OEM), YourMechanic professionals in certain locales can assist with that. Please simply inquire based on your locale. If you have further questions or concerns, do not hesitate to re-contact YourMechanic.