Methods or any innovative ways to check the correct layer order independent of the customer given layer stack data
I am a strong proponent of putting readable layer indicators on each layer that can be seen through the board after it is fabricated. Such markings, when done correctly, can be used to very quickly determine that all layers are in the correct place. Here is an example of how these could look for an 8 layer board. On layers with internal plane fills the plane is cut back away from the layer indicators and the outer solder mask contains an opening on each side over the marker area. 



Once the board is all fabricated the layer markers appear as follows and can be easily seen when the blank board is held up in front of a light source.



This scheme also is useful for sorting layers of Gerber films and the best part of it is that it is totally under the design control of the customer.