If you have an aclocal.m4 installed with Autoconf (as opposed to in a particular package's source directory), you must rename it to acsite.m4. See autoconf Invocation.
If you distribute install.sh with your package, rename it to
install-sh so make builtin rules don't inadvertently
create a file called install from it. AC_PROG_INSTALL
looks for the script under both names, but it is best to use the new name.
If you were using config.h.top, config.h.bot, or
acconfig.h, you still can, but you have less clutter if you
use the AH_ macros. See Autoheader Macros.