1) Just copy all nvidia's headers over to /usr/include/GL. Note that to compile GL apps more headers are needed for example from Mesa since nvidia doesn't provide all headers.
2) Normally the GL libraries are installed to /usr/lib, are you sure the libraries in /usr/X11R6/lib are not the ones from xfree86? If not keep the symlinks or just move the files over.
3) There are two types of libraries on linux static (.a) and dynamic (.so). Most applications use dynamic libraries. When you build an app using static libraries the library gets builtin into the app. In such a case you can copy the app to another system and the library is not needed.
In general you don't need these static libs and likely nvidia can't provide them because of legal reasons. (linking a GPL'ed app with a static lib ..)
Really remove libGL.a if you have it left. If it doesn't exist apps will use the dynamic library.