George,
It sounds like the approach you are using is the correct one. This seems to be the cleanest solution to me especially since the customer is able to modify the generated SQL statements for their new system.
In order to preserve the AutoInc values I would recommend altering the table and changing the field datatype from AutoInc to Integer. Then export the table as code which will export the actual values. After the tables have been created on the new system they can change the field datatype back to an AutoInc type if necessary.
Regards,
Chris Franz