In my opinion, you can simplify a bit the configure script by using AC_TYPE_LONG_LONG_INT for detecting the support of long long type. The sources using HAVE_LONG_LONG just need to use HAVE_LONG_LONG_INT instead.
True, this code was added long before AC_TYPE_LONG_LONG_INT existed, and it looks like it has been supported since autoconf 2.60 at least, so it'll be "safe' to start using it now.
In my opinion, you can simplify a bit the configure script by using AC_TYPE_LONG_LONG_INT for detecting the support of long long type. The sources using HAVE_LONG_LONG just need to use HAVE_LONG_LONG_INT instead.