I'd check that OpenGL installed.
"glClipPlane" is defined in /usr/openwin/lib/libGL.so.1 on my system:
nm /usr/openwin/lib/libGL.so.1 | grep glClipPlane
[4708] | 359444| 72|FUNC |GLOB |0 |10 |glClipPlane
libJ3D.so has a dependency on libGL.so.1
$ ldd libJ3D.so
libdga.so.1 => /usr/openwin/lib/libdga.so.1
libdl.so.1 => /usr/lib/libdl.so.1
libGL.so.1 => /usr/openwin/lib/libGL.so.1
...
One minor thing I'd avoid is modifying the contents of packaged software
unless replacing the package with new packages. In the case of /usr/j2se
I leave it alone and maintain a separate directory with whatever the
latest jvm is e.g. /usr/j2sdk1.4.2_03
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