We have a great tool in AX 2012 for upgrading EDT relations to the new structure of Table relations.

Unfortunately it does not handle system data types like UserId very well. You have to change the \Classes\SysEDTMigration to prepare the tool for all types:

public boolean migrateToNewRelation(
    tableName _tableName,
    fieldName _fieldName,
    SysEDTMigrationEDT _edtInfo,
    boolean _deleteAction)


    fkTableNode = TreeNode::findNode(strfmt('%1\\%2',#TablesPath,_tableName));
    edtNode = TreeNode::findNode(strfmt('%1\\%2',#ExtendedDataTypesPath,_edtInfo.Name));

//--> WIK
    if (!edtNode)
        edtNode = TreeNode::findNode(strfmt('%1\\%2', #SystemTypesPath, _edtInfo.Name));
//<-- WIK

You can find more details on MSDN about the EDT Relation Migration Tool: