You can provide all necessary additional files (mxds) in a zip archive. To further protect them you can set password for such archive or compare checksums.
In order to do it you need to create and use python script in your module. Just write script which will unzip your mxds to some temporary folder (you can pass this folder and zip file as an input parameter for your script). Then add this script to your Toolbox and use it in you model in Model Builder.
Another way is to export your whole model to python and perform further development there. I am usually prefer this way in cases when I am facing additional more complex processing tasks and have needs in other libs.
There is even one more way: you can create python script for ArcToolbox which will accept all needed input parameters then unzip your mxds and execute your custom model (the one you have now), then perform all cleaning (of unziped files). In such way you just changing entry point for your processing task.
Here is some points to start from: