I came up with a solution that just works. It isn't pretty or efficient, but it does work.
In all cases, I know that my edges have two termination points. This means that there are no circles, forks or branches.
Then, I first find the endpoints of each component using the 'endpoints' option in bwmorph().
Picking one endpoint, I check the 8 neighboring pixels in the order N,E,S,W,NE,SE,SW,NW (to ensure 4-connected pixels are given priority), set the current pixel to 0 and repeat it for the pixel I found among the neighbors. This continues until the other endpoint is reached.
By saving the coordinates of each pixel as it is set to 0, I have a list of connected pixels.
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