Awesome. I'm not sure about those "floating" bones (I have seen them and ignored them myself). They're either something to do with weapon attachment, or they're leftover badly-translated IK handles. I don't think they're meant to attach to any of the body vertices.
l_handle_1 and R_handle_1 are attached to the skeleton, but not connected to any vertices in the hand.
L_Handle_ and R_Handle_ are floating loose, and not connected to anything on the body. In most of the animation files, they don't exist - though they are connected to the placeholder guns in some files.
I think only Karpov can explain what these are - unless we can work it out by studying and testing the files.
This should be an .x file with a handful of human animations in it :
CR_humananims.X. If you can export/import/merge that into the file you're using, you should be able to test some of the existing animations to make sure everything works. In those, have a look at the unconnected "handle" bones and see what they do.
You can download the other animations individually from the main 3D repo here :
FOnline3d (look at male_rifle.x for example of placeholder weapon attachment).
Also - yes, we definitely need a unified mesh / animation which will work across multiple programs, and it does need to be the same one for compatibility - ideally where we can put a file in Max, Fragmotion or Blender (and others if possible). However, that tutorial is very clear to help with understanding how the rigging works and would be useful for either modifying or correcting existing ones, or for adding new ones like dogs, geckos, rats etc. For the main human though, we need a working version of the original model and animations in Blender - which is exactly what you seem to be doing, and I thank you very much for this. I tried to do this myself years ago, but failed.
Next test of course would be to try and export something from Blender and see if it will work in game (If you don't have an SDK set up yourself, upload it here and I'll test it). Test something basic like replacing the default idle pose, or replacing the default walk with a
Silly Walk.