the tools you are looking for are 'gdal_translate' and 'gdalwarp'. You can find it in the FWTools2.4.7\bin folder.
With gdal_translate you can set upper left and lower right coordinates of your scanned image and, if you want to, assign a spatial reference system.
With gdal_warp you can reproject that image to any other spatial reference system.
For specification look at http://www.gdal.org/gdal_translate.html and http://www.gdal.org/gdalwarp.html.