Sorry I don't have time to do better than point you at:
http://www.gnu.org/software/automake/manual/automake.html#Scripts
and the way we use for NTP is a bit nastier, as we support installing
programs and scripts into configure-specified directories based on the
OS (for legacy reasons). But I also do not use the "do_subst" trick
there; I name the files scriptname.in and let configure do the
substitutions for me, which means I pretty much only need bin_SCRIPTS in
the Makefile.am. Since the "source" for the script is scriptname.in, I
don't have to wory about DIST issues. I don't care about CLEAN issues,
either. If I did I'd add ${bin_SCRIPTS} to CLEANFILES.
H