Follow these steps, will help you.
1.Firs of all run the duplicate detection form
2. than upgrade column List
3. copy the command from left justified form
4. use installation file to setup a new ax 2009 database.
5 run the pre-databaseupgrade tool, move data from ax 3 to ax 2009 database created at step 4.
6. execute the command from step 3 on sql server. (faster performance)
7. install AOS, sp1 and ru6, point to the database created at step 4.
Regards
D