PDF's from Illustrator not been replaced in layer in ID...

Hi,
I want to place PDF into new layers in an InDesign document. All the layers are the same data (map) but they are not scaled... Like when you press Command + D to place something into InDesign you have to scale it yourself...
The document that I'm working with already has the object scaled, but when I place new layers (of the same map) I have to manually adjust each box and scale...
I have around 8 layers that need to match up to each other which is going to take a very long time (as the map is big)
The solution I found that worked (for 1 layer) was to just duplicate the original layer eight times (that already has the scale etc.), importing different pages of the PDF but by replacing the selected item which keeps scaling and rotation attributes. This worked great for one layer, which was a layer of the map that had already been made by a professional. I simply added more layers to the same map, which is where I'm having problems when placing inside ID. The layers simply will not scale, even though they are the same file format etc. as the layer that did work.
I've used the size and X/Y coordinates but that hasn't worked for some reason...
Thank You

I'n Using CS5.
Screenshots:
The 1st coloursed one is Illustrator. The map has multiple layers, the first one is a black outline of cities and roads. The next layers are all colour, showing the types of roads shops etc. All these layers were created on top of a DWG. file that I was provided with... I just opened it in AI and saved as PDF. The layers where created just by clicking the new layer icon.
http://dl.dropbox.com/u/1055166/AI.png
I saved ALL layers as a PDF and opened it inside ID to scale and add a key.
I now want to have each layer from AI on it's own layer in ID so that I can print each layer seperatley (on acetate), but since the original layer has been scaled already, I should use that one. (but can't because it's one PDF with one layer.)
I opened the already created ID document and copied the layer. I then changed the layer to a PDF exported from AI (the 'main B&W one), replacing the original content. The scale orientation etc, matched perfectly on this layer.
I exported the coloured layers from AI in the same fashion (PDF) but when I use the same technique of replacing content in ID, the scale does not match...
The second coloured screenshot (less page fill) is Indesign. It shows the original exported document (with no individual layers) from AI.
http://dl.dropbox.com/u/1055166/ID.png
Again, it seems to be the layers that I have added that are causing the problems. I know I can manually adjust each PDF from each layer, but as its a large map and many layers, it will take some time.
The black and white screenshot shows a reference to the whole map.
http://dl.dropbox.com/u/1055166/main.png
Lastly. The reason I want to use ID for my page layout instead of AI is because I find it much easier and I already have a scale etc. on a ID document.
Thank You
EDIT: I don't suppose there is a converter for AI documents to be readable in ID WITH all the layers? That would make it so much easier.

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