Autoconf is supposed to make life easy, I guess that

is only true if someone else sets it up for you.
Here's my fumbly finger approach to get it right.

admin-root/lib-js/Makefile.am

@@ -2,7 +2,7 @@
 #
 SUBDIRS=script.aculo.us
 
-jslibdir = ${pkgdatadir}/lib-js
+jslibdir = ${pkgdatadir}/admin-root/lib-js
 jslib_DATA = prototype.js
 EXTRA_DIST = prototype.js
 

admin-root/lib-js/script.aculo.us/Makefile.am

@@ -1,6 +1,6 @@
 # $Id: Makefile.am 712 2005-11-20 10:02:31Z rpedde $
 #
-scriptaculousdir = ${pkgdatadir}/script.aculo.us
+scriptaculousdir = ${pkgdatadir}/admin-root/lib-js/script.aculo.us
 scriptaculous_DATA = builder.js controls.js dragdrop.js effects.js \
                      scriptaculous.js slider.js unittest.js