For the blank CR2 (donor bones figure): leave the channels in, but take any deltas out, they'll be useless with different geometry (as you've already realized).

Skirts are pretty much impossible to rig the same way as the figure, as there is simply no way to group the polygons below the hip such that you will a) get remotely realistic deformation and b) have the same bone structure as the legs.  A given bone can deform its own polygon group, or its parent; so, if you have bones for hip -> thigh -> shin, then in order for the shin bones in the skirt to do anything, they cannot be children of the thigh; or you have to come up with a polygon grouping for the skirt where the hip goes to the floor (will look very wrong when the shin is bent).  You're welcome to look at some of the skirt rigs I've published in my freebies, particularly the dark sorceress dress; all bones below the hip are children of the hip.  This does not and cannot follow the character's leg movements but it's at least flexible enough to get some amusing movements out of the skirts.

My Freebies