after upgrading libtool to 1.4 i have upgraded automake and autoconf to latest stable versions, here is the result:

buildconf: checking installation...
buildconf: autoconf version 2.50 (ok)
build/buildcheck.sh: test: 4-p1: integer expression expected
buildconf: automake version 1.4-p1 (ok)
buildconf: libtool version 1.4 (ok)
WARNING: automake and libtool are installed in different
         directories.  This may cause aclocal to fail.
         continuing anyway
rebuilding Makefile templates
automake: configure.in: installing `Zend/ylwrap'
rebuilding configure
./aclocal.m4:904: error: m4_defn: undefined: _m4_divert_diversion
./aclocal.m4:452: PHP_SUBST is expanded from...
./aclocal.m4:904: the top level
rebuilding acconfig.h
rebuilding main/php_config.h.in
autoheader: error: shell error while sourcing /tmp/ah26273/traces.sh

in build/buildcheck.sh:
first problem - automake version is 1.4-p1 and this check fails:
IFS=.; set $am_version; IFS=' '
if test "$1" = "1" -a "$2" -lt "4" || test "$1" -lt "1"; then

fix:

Index: build/buildcheck.sh
===================================================================
RCS file: /repository/php4/build/buildcheck.sh,v
retrieving revision 1.8
diff -u -r1.8 buildcheck.sh
--- build/buildcheck.sh 2001/05/06 18:51:21     1.8
+++ build/buildcheck.sh 2001/05/22 00:25:01
@@ -40,7 +40,7 @@
 fi
 
 # automake 1.4 or newer
-am_version=`automake --version 2>/dev/null|head -1|sed -e 's/^[^0-9]*//' -e 's/[a-z]* *$//'`
+am_version=`automake --version 2>/dev/null|head -1|sed -e 's/^[^0-9]*//' -e 's/[a-z]* *$//' -e 's/-/./'`
 if test "$am_version" = ""; then
 echo "buildconf: automake not found."
 echo "           You need automake version 1.4 or newer installed"

second problem - 

after double checking for libtool, $libtool is set to `which libtool` or `which glibtool`. in the check if libtool and automake are in the same path again which is used that is incorrect because which /bin/libtool founds nothing.

fix: 

Index: build/buildcheck.sh
===================================================================
RCS file: /repository/php4/build/buildcheck.sh,v
retrieving revision 1.8
diff -u -r1.8 buildcheck.sh
--- build/buildcheck.sh 2001/05/06 18:51:21     1.8
+++ build/buildcheck.sh 2001/05/22 00:30:21
@@ -81,7 +81,7 @@
 fi
 
 am_prefix=`which automake | sed -e 's#/[^/]*/[^/]*$##'`
-lt_prefix=`which $libtool | sed -e 's#/[^/]*/[^/]*$##'`
+lt_prefix=`echo $libtool | sed -e 's#/[^/]*/[^/]*$##'`
 if test "$am_prefix" != "$lt_prefix"; then
     echo "WARNING: automake and libtool are installed in different"
     echo "         directories.  This may cause aclocal to fail."

i'd update this bug when i find what else is going wrong