Q: can a 2006 automatic engine fit into a 2002 manual 325i?

I looked up the two applications. Those two engines use completely different castings for both the heads and the block and the flywheel (flex plate) is different as well which will make it incompatible with your transmission. If you search at Car-Part.com you will find an exact match for your car. Engine swaps on modern computer controlled vehicles must be exact matches because if you attempt to use an engine that is not cataloged as a direct cross reference for your car or truck, you will find that the engine computers are not interchangeable. Consequently, even if you can get a "different" engine to physically fit, it won’t start and run. And, you cannot flash re-program your existing computer to work with a new engine because all of these engines use different computer hardware, that is physically different PCM’s. In addition, the engine wiring harnesses are completely different, and the TCM (transmission control module) will have to be completely changed as well. As if that isn’t enough, if and once you substitute a new PCM and TCM they won’t work seamlesly, if at all, with the other computers on the vehicle such as the body control module but there are many other microprocessors involved as well. In the modern era, really the only way engine swaps using non cataloged, non interchangeable engines can work is if you literally carry over all electronic controls and wiring that are associated with the engine and the vehicle to your vehicle. If you are interested in an OEM (cataloged, direct interchange) engine/transmission replacement, 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. If you have further questions or concerns, do not hesitate to re-contact YourMechanic.