I finally have an excellent capture of each of the three LDs. It's one tremendous (415GiB) 10-bit v210 (YUV422P10LE) file.
This took more time than I expected because of minor undocumented things, such as the fact that the Blackmagic Intensity Shuttle sets its gain based on the first frame it receives. My solution to this is to turn off the Runco LJR-II's fluorescent display before turning the computer on to ensure that the first frame the Blackmagic Intensity Shuttle receives is a completely black one.
The transfers were done completely flat with the pre-amp set to 0dB gain for Y and C. I could have calibrated it using the color bars on GGV1069, but I decided against this since what I really want is the closest digital approximation of the Runco LJR-II's s-video output. Plus, the aforementioned gain issue really screwed with my attempts to calibrate and it got too frustrating.
I'm currently working on temporal alignment and it's going well. The Runco LJR-II—believe it or not*—occasionally inserts a duplicate frame, but this is easy enough to detect and fix. This is where Avisynth's Subtract function really shines.
And, yes, I said Avisynth. I'm really happy with the colors as they are, so I felt comfortable dropping to 8-bit Huffyuv (YUV422P) for post.
(* I know it's the Runco LJR-II rather than the capture card because, if it were the capture card, the duplicate frame would be bit-for-bit identical, but it's not.)