The files X, X11, and X11R3 in the /usr/bin/X11 directory contain
references to the /usr/bin/X11 and /usr/lib/X11 directories. There are
several ways to get around this. You could add the environment variables
$X11BINDIR and $X11LIBDIR to your .login or .profile files, setting them to
the location of the new X lib and bin directories. If you are using the
Bourne shell you would then export them, or if you're using the csh you
would create them as environment variables (that is, with setenv(1)). You
could also just link the new directories to the old locations, making
symbolic links between the old and the new. Or you could modify the
/usr/bin/X11/[X X11 X11R3] scripts to reflect the new directory locations.
Any of these procedures should solve your problem.