Will the engine from a 2005 Crown Victoria fit a 2001?
The Long Block will work fine. You will need to swap out the Oil Pan, Intake etc but as for the base engine itself - yes it will.
Research the vehicle specifications online. The only difference is long and short block and transmission (automatic or manual). Same motor. 4.6 liter V8. To be accurate measure!
Do I use the computer and wire harness from the 06 or the one off the 01
There are statistics available online just put the same question to your computer, area and make, model year of vehicle. Wiring harnesses are often part specific. If you are changing parts from 06 to 01 or vice versa the hardware used should adapt to the motor and electrical specs of the vehicle to reprogram computer, etc.
Check the wiring diagrams for the year of vehicle. There are different harnesses for different parts. Calling or visiting a parts store, or the dealership so as to not cause a fire under hood or dash would be a good idea. Check part numbers and compare online with harness part numbers as long as they can be paired together you should be safe. Length of these harnesses can be key when changing from long block to short block. Measure, check ends, voltage capacities, etc. Tedious yet worth it when finished. Electrical parts vs. mechanical. Hope this helps!
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