Hi Kir!
I understand exactly what you're problem is, but see, I also have a problem too -- I'm shit for explanations. So, please excuse me if you don't fully understand and I'll give it a go with visuals later:
You're issue is that the when you copy the Body/Bottom Template Mod(s) the child movie clips are not also being duplicated, only the parent movie clip (henceforth MC). So when you double click and enter that duplicated MC all the other MC's inside are still the same and are respectively linked between the duplicated parent and original parent MC.
The solution is to duplicate ALL MCs associated with the the clip you want to duplicate.
So, let me try to walk you through it:
1a.) Duplicate the Right Thigh Clip (Right Thigh Body in Kona's temp) and pop it down on a new layer. There are now no child movie clips -- so, just give the new Thigh the appropriate instance name you're good to go!
1b.) Duplicate the Bottoms Template/Body mod if you require different settings or want to separate the "rightThigh" and "rightThighMasked" instances. (This MC has assets).
2.) Duplicate the Right Thigh Body MC inside your newly duped parent MC - rename it to whatever.
3.) Give your duped Right Thigh Body MC the instance name "rightThighMasked".
4.) Win at SDT.