I'm doing it the easy way. Rather than rifle through folders and try and figure out what files belong to what item, I just deleted the runtimes that I wanted to redo and start with a clean slate. That way I can take time to pick and choose what I want to add or keep out. I take the time to install/unzip one file, then go to the library/character, and library/pose folders and further organize them there, before moving onto the next file. It's slow going, but at least I know that I'll be able to find the readme's and MAT files that go with the clothing item from the character folder, because I've named them the same and have grouped all of the MATS for an item in a common folder for that item in the Poses folder IE: all my MATS for MFD are located in the MFD folder (one stop shopping when working with MFD) I'm not comfortable separating all textures to it's own folder/runtime yet. I'll see how what I'm doing goes, and maybe the next time I have to redo my runtimes, I'll try something a bit different to further organize the files. But for now I'll either do the common multiple character files runtime, or install the item into each figure's runtime. I don't have a lot of hard drive space to work with, so duplicate files are a concern to me, however, I will be storing my unused runtimes on a CD and swapping them back and forth from CD to hard drive as I need them. I'll keep hair, poses, faeries and lighting as constants on my main hard drive, and swap out the figure ones as I need them.

"It is good to see ourselves as others see us. Try as we may, we are never
able to know ourselves fully as we are, especially the evil side of us.
This we can do only if we are not angry with our critics but will take in good
heart whatever they might have to say." - Ghandi