The grayscale .jpg is the actual orthophoto you can use as a reference decal for the track, or to use for reference when making a high-res color one.
The .jpgw file is what is commonly refferred to as a world-file; it's a plain text-file that contains the orthoreference information for the .jpg image i.e. the coordinates for the top left pixel in the image and the scale of each pixel.
The .prj files contains info about the datum i.e. what geographic coordinate system the coordinates in the world-file are in.
If you would open a file with the elevation data for, say the whole of Spain, in a GIS e.g. Mapwindow, the .jpgw and .prj files above makes it possible to place your .jpg orthoimage as an overlay in exactly the right place automatically.
I suggest reading the excellent explanation of the files
here.
In this case you'll need the information in the .jpgw file to cut out the exact same area from the SRTM elevation in Microdem using the tool "Keyboard corners" that you can access by RMB->Modify map area->Keyboard corners.
Just put your calculated coordinates from the world-file in the appropriate boxes and the map image should cover the exact same area as your orthoimage.
Make sure that both the orthoimage and the SRTM data uses the same datum first though, if not you'll need to convert the image to the same datum as the SRTM dataset. If I remember correctly you can do that in Microdem as well.
From looking at the image in your post I'll suggest that you export a new image from Google Earth that covers a much larger area.
You can always cut it down to size later in Photoshop together with your base terrain from Microdem.
Just make sure it's possible to make out enough detail to enable you to align a high-res orthophoto later.