I'm just catching up with this ancient post, but if anyone is still interested, I'll add a few more bits:
Until several years ago, a large frame house stood alongside the canal and original railroad bed just south of where Alexander St. crossed. This was originally a railroad/canal hotel and, we believe, also served as the C&A passenger station. Unfortunately it became too decrepit to save (despite some efforts to do so), and was razed.
Not much farther north, at the point where the canal crossed the Millstone River, a line of piers still remain, and it's likely these were used by the railroad. If so, they may be the only surviving remnants of the rail line.
The original line turned away from the canal just south of Kingston and ran overland to what was later Deans station, north of Monmouth Jct., where it joined the later "straight line." As noted, most of this section survived as part of the Rocky Hill branch, and at some point -- I have no idea when -- it was cut back to join the relocated line at Monmouth Jct.