Make as many artboards as you have layers.
select the art on a layer easiest way is to use the layers panel.
Command C to copy
refocus on the artboard with the same number as the layer or if the layers have names, name the artboards accordingly and select to match that way.
then command shift V to place in place the art will be pasted in the same position on the artboard as it was on artboard one or relative to the original.
when you have all the artboards with their content in place save it as a pdf. using the use artboard feature select all or a range
and now you have a multipage pdf.
yes I know this not what you want but in the future just remember this is how it works and be prepared to have an artboard for each layer.
And it is not that much work to do this.