It is a lot of work,but you may try this:
Open the PDF in Adobe Acrobat, save as many different files as you want layers.
For each layer you need to remove the other ones in Acrobat:
Open the file for the first layer. Select > View > Show/Hide > Side panels > Layers. Hide all the layers except the first one. From the Options menu, select Flatten Layers. Save the file and repeat for the other layers. In Illustrator create a file at the size you need. Create as many layers as you need. Open the first pdf in Illustrator and copy the content. Select the first layer in your Illustrator file and choose Paste in Place Repeat for the other layers.
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