I've just joined this thread, so let me know if I get out of line.
I've had the opportunity to walk almost all of the old track bed between the old depot in Santa Fe and the Otowi Bridge over a period of a year or two. I live on Rio Grande which used to be the track bed. I've also walked most of the route between Embudo and Baranca, half of ti up from Embudo and the other half down from Baranca - it's posted as a private road towars the bottom so I tried to be unobtrusive.
I saw either this culvert or one very much like it. It seems as if there were several. Huge logs. There are also several piers still in place from the bridges across arroyos.
You made reference to Milepost 388.3. I realize that trains use such designations and mark them as such along the tracks, but how do you know now which mile marker you are at now? We found a site that was probably Jacona but I don't know how to tell where we were.