It seems I was wrong. I was told years ago by somebody (and 'old crank with a failing memory', it seems....) that the R&E crossed the Auburn road, the followed alongside French rd. until the edge of the village of Pittsford. I have a framed county-wide topographic map from about 1911 that is....well, unclear as to where the R&E went, and with roads, rail rights-of-way and topographic lines all coming together, I believed that narrative.
However, it seems that there are a couple of things about the R&ERR that I can say with some certainty now. Firstly, was that it followed Monroe Ave pretty much from downtown (save for the last decade or so, when it used the subway right-of-way) all the way until it veered off into the fields at roughly where the old Graphlex plan is today, just before the embankment that takes you up to the canal bridge. From there, it went under the Auburn road, along it's own right-of-way, which brings up into the map of Pittsford village posted just above.
Today, I went out on a quest to find it. The first photo shows the route from just next to the end of the old pickle factory. The second shows the northern side of the embankment on the Auburn road. The third shows the view southward, with the brand-new hiking trails that were put in just this summer, and the 4th photo, well, there it is; the same view as the original picture!
Notice the fence gate in the distance above; it's the same one you see in the distance below.
Tis is looking sout-eastward, over where the track used to go straight towards Monroe,
And, this is a picture from almost exactly the same location (a few feet closer, since that location is now in the middle of a swamp.
What they did with the old R&E track was this: they turned it into a drainage culvert. There is a large corrugated pipe under all that fill where the bridge used to be, and it looks like whatever ballast there once was has been bulldozed of backhoed, making the entire area between this underpass and the old Graphlex plant pretty much a wetlands. It seems that all the drains on all the parking lots around the DelMonte spa, under the WEST shore overpass (sorry, I always consider that the only shore near it is the SOUTH shore of Lake Ontario...), and the pickle factory all run straight into this area.
This also answers another mystery, namely, why did the NYC allow a direct competitor underground access to cross their property? Probably, there was already a culvert there, and the R&E offered to revamp the area, then maintain it. Probably saved the NYC a ton of $$.