Can I place a caption in the second column next to a long, full-column-wide figure?
No, unfortunately the REVTeX 4.1 layout isn’t that sophisticated. When there are two figures on the same page, the second one doesn’t seem to appear. Please check your log file. You should be receiving error messages; i.e., could not place figure, or something similar. It should not just be ignoring the figure. You can try the floatfix option and see if that helps.