1995 Trenton West, NJ
1995 Trenton East, NJ
And a 1/9 DEM of the area: Fairless_t.zip (~40MB)
Summary:
The 2 PDFs seem to load into TransDEM OK, but the transparent margins do not line up at all. I thought this might be due to the 1947 historical PDF problem some of us have encountered, so I edited the XML file in the TransDEM temp folder and manually changed the projection from "Transverse Mercator" to "Polyconic". Unlike the 1947 PDFs, which continue to georeference correctly and automatically at this point, these 2 1995 PDFs bring up a dialog in TransDEM that asks me for the Coordinate System. Well, I chose "Polyconic / NAD27" and continued. This seemed to work as the transparent margins lined up well and the raster maps were placed over my DEM properly. Almost. Upon closer inspection, I noticed there is approximately a 215 meter offset between the raster map and the DEM. I created a tiny route from a Google Earth kmz file as a sanity check and that lines up with the DEM, so I know the DEM is correct:

The only thing I can think to do at this point is to manually georeference the raster map. I don't have much experience doing this, so I've been procrastinating. I thought I'd post here to see if anyone else has a suggestion.
Oh, I did try a few of the other Coordinate Systems in the dialog that came up, but they badly rotated the raster maps and placed both in the same place.
May I offer a feature that might be nice for a future enhancement to TransDEM? Once I've reached the point in the above screenshot, the ability to drag (and finely rotate, if necessary) the raster map in TransDEM, would be another very easy (possibly lazy) way to manually line up the raster map to the DEM.
Thanks for your assistance.
Andrew