Okay, two things. First, you'll note that the ESP file aren't included in the bottom section that lists "currently installed files", so that's why they aren't in your load order.
Second, without a script to handle the install, I believe you need a simpler structure. The two ESP files should be in the "base" of the omod (the main directory, not in any other subdirectory), and the nif files should only be in the files beginning with Data. So it will look like this in the report:
Spoiler [Complete plugin list]
RealisticMagicForceLow.esp
RealisticForceMedium.esp
[Complete data file list]
Data\meshes\creatures\zombie\skeleton.nif (54F0DA56)
Data\meshes\creatures\xivilai\skeleton.nif (4BBED527)
Data\meshes\creatures\troll\skeleton.nif (81AC0B7A)
Data\meshes\creatures\spriggan\skeleton.nif (FBB6E383)
Data\meshes\creatures\spiderdaedra\skeleton.nif (D8C468F8)
Data\meshes\creatures\slaughterfish\skeleton.nif (71865E09)
Data\meshes\creatures\skeleton\skeleton.nif (30CFEBBE)
and so on.