This process explains if a customer that owns a Boxster from 2003 can add a 996 3.6 liter engine into their car. The answer yes it is possible and should be done with a lot of care. To do so:

We highly recommend that you also bring the ECU from that 996 and the engine harnesses because the cars are from completely different generations, with varying features, ECU numbers, programming, features, additional wiring, and sensors, etc.

We can still reuse the immobilizer and key fobs from the 2003 Boxster and bind these with the 996 engine.

Normally, when you do engine swaps they go well but sometimes ECU is not properly calibrated with the engine. We can easily remap the ECU and the engine for optimum performance of the car.