Index: pym/portage_util.py
===================================================================
--- pym/portage_util.py	(revision 5113)
+++ pym/portage_util.py	(revision 5115)
@@ -489,7 +489,7 @@
 	return u
 
 def apply_permissions(filename, uid=-1, gid=-1, mode=-1, mask=-1,
-	stat_cached=None):
+	stat_cached=None, follow_links=True):
 	"""Apply user, group, and mode bits to a file if the existing bits do not
 	already match.  The default behavior is to force an exact match of mode
 	bits.  When mask=0 is specified, mode bits on the target file are allowed
@@ -502,7 +502,10 @@
 
 	if stat_cached is None:
 		try:
-			stat_cached = os.stat(filename)
+			if follow_links:
+				stat_cached = os.stat(filename)
+			else:
+				stat_cached = os.lstat(filename)
 		except OSError, oe:
 			func_call = "stat('%s')" % filename
 			if oe.errno == errno.EPERM:
@@ -517,7 +520,10 @@
 	if	(uid != -1 and uid != stat_cached.st_uid) or \
 		(gid != -1 and gid != stat_cached.st_gid):
 		try:
-			os.chown(filename, uid, gid)
+			if follow_links:
+				os.chown(filename, uid, gid)
+			else:
+				os.lchown(filename, uid, gid)
 			modified = True
 		except OSError, oe:
 			func_call = "chown('%s', %i, %i)" % (filename, uid, gid)
@@ -548,6 +554,19 @@
 		if mode != st_mode:
 			new_mode = mode
 
+	# The chown system call may clear S_ISUID and S_ISGID
+	# bits, so those bits are restored if necessary.
+	if modified and new_mode == -1 and \
+		(st_mode & stat.S_ISUID or st_mode & stat.S_ISGID):
+		if mode == -1:
+			new_mode = st_mode
+		elif mode & stat.S_ISUID or mode & stat.S_ISGID:
+			new_mode = mode & 07777
+
+	if not follow_links and stat.S_ISLNK(stat_cached.st_mode):
+		# Mode doesn't matter for symlinks.
+		new_mode = -1
+
 	if new_mode != -1:
 		try:
 			os.chmod(filename, new_mode)
@@ -614,7 +633,7 @@
 	return all_applied
 
 def apply_secpass_permissions(filename, uid=-1, gid=-1, mode=-1, mask=-1,
-	stat_cached=None):
+	stat_cached=None, follow_links=True):
 	"""A wrapper around apply_permissions that uses secpass and simple
 	logic to apply as much of the permissions as possible without
 	generating an obviously avoidable permission exception. Despite
@@ -625,7 +644,10 @@
 
 	if stat_cached is None:
 		try:
-			stat_cached = os.stat(filename)
+			if follow_links:
+				stat_cached = os.stat(filename)
+			else:
+				stat_cached = os.lstat(filename)
 		except OSError, oe:
 			func_call = "stat('%s')" % filename
 			if oe.errno == errno.EPERM:
@@ -653,7 +675,8 @@
 			all_applied = False
 			gid = -1
 
-	apply_permissions(filename, uid=uid, gid=gid, mode=mode, mask=mask, stat_cached=stat_cached)
+	apply_permissions(filename, uid=uid, gid=gid, mode=mode, mask=mask,
+		stat_cached=stat_cached, follow_links=follow_links)
 	return all_applied
 
 class atomic_ofstream(file):
Index: pym/portage.py
===================================================================
--- pym/portage.py	(revision 5113)
+++ pym/portage.py	(revision 5115)
@@ -1344,6 +1344,16 @@
 			self["PORTAGE_PYM_PATH"] = PORTAGE_PYM_PATH
 			self.backup_changes("PORTAGE_PYM_PATH")
 
+			for var in ("PORTAGE_INST_UID", "PORTAGE_INST_GID"):
+				try:
+					self[var] = str(int(self.get(var, "0")))
+				except ValueError:
+					writemsg(("!!! %s='%s' is not a valid integer.  " + \
+						"Falling back to '0'.\n") % (var, self[var]),
+						noiselevel=-1)
+					self[var] = "0"
+				self.backup_changes(var)
+
 			self.regenerate()
 			self.features = portage_util.unique_array(self["FEATURES"].split())
 
@@ -2614,6 +2624,29 @@
 
 	if phase_retval == os.EX_OK:
 		if mydo == "install":
+			# User and group bits that match the "portage" user or group are
+			# automatically mapped to PORTAGE_INST_UID and PORTAGE_INST_GID if
+			# necessary.  The chown system call may clear S_ISUID and S_ISGID
+			# bits, so those bits are restored if necessary.
+			from itertools import chain
+			inst_uid = int(mysettings["PORTAGE_INST_UID"])
+			inst_gid = int(mysettings["PORTAGE_INST_GID"])
+			for parent, dirs, files in os.walk(mysettings["D"]):
+				for fname in chain(dirs, files):
+					fpath = os.path.join(parent, fname)
+					mystat = os.lstat(fpath)
+					if mystat.st_uid != portage_uid and \
+						mystat.st_gid != portage_gid:
+						continue
+					myuid = -1
+					mygid = -1
+					if mystat.st_uid == portage_uid:
+						myuid = inst_uid
+					if mystat.st_gid == portage_gid:
+						mygid = inst_gid
+					apply_secpass_permissions(fpath, uid=myuid, gid=mygid,
+						mode=mystat.st_mode, stat_cached=mystat,
+						follow_links=False)
 			mycommand = " ".join([MISC_SH_BINARY, "install_qa_check"])
 			qa_retval = spawn(mycommand, mysettings, debug=debug, logfile=logfile, **kwargs)
 			if qa_retval:
Index: bin/misc-functions.sh
===================================================================
--- bin/misc-functions.sh	(revision 5113)
+++ bin/misc-functions.sh	(revision 5115)
@@ -182,17 +182,6 @@
 		unset INSTALLTOD
 	fi
 
-	local find_log="${T}/find-portage-log"
-	find "${D}"/ -user portage -print0 > "${find_log}"
-	if [[ -s ${find_log} ]] ; then
-		xargs -0 chown -h ${PORTAGE_INST_UID:-0} < "${find_log}"
-	fi
-	find "${D}"/ -group portage -print0 > "${find_log}"
-	if [[ -s ${find_log} ]] ; then
-		xargs -0 chgrp -h ${PORTAGE_INST_GID:-0} < "${find_log}"
-	fi
-	rm -f "${find_log}"
-
 	# Portage regenerates this on the installed system.
 	if [ -f "${D}/usr/share/info/dir.gz" ]; then
 		rm -f "${D}/usr/share/info/dir.gz"