Couple of things (list is not comprehensive) too look out for, other e46 owners please feel free to add:-
1. Jap specs cars have differenct CO2 emission standards and so wear and tear is slightly different.
2. Check the Control Arms/ Lower Arms. A 5 year UDM will wear out the bushings etc
3. Oil Sump. Check for leaks/cracks. Make sure the undercarriage "plate" is intact
4. Mods on the cars. As Japanese cars are usually modded vehicles (as evidenced by the number of e46's which "arrive" in malaysia with various bodykits/alloys/etc) check for engine wear&tear. A heavily run car will give you issues.
5. Do the usual Puspakom checks to ensure the car isnt a "kereta potong" or that its been in a major accident.
6. Check the mileage! The meter might have been tampered so if possible, use the ignition key to verify the milage. However, its now a little more troublesom as even the mileage from the keys can be manipulated!
Lastly, contact RedEarthfor details on e46 sifu's who might be able to assist you in picking out a good car.
Good luck!