Set the proper file permissions and symlinks by running:
chmod 755 rcS reboot halt mountfs umountfs
chmod 755 sendsignals checkroot sysklogd setclock
cd ../rc0.d
ln -s ../init.d/sysklogd K90sysklogd
ln -s ../init.d/sendsignals S80sendsignals
ln -s ../init.d/umountfs S90umountfs
ln -s ../init.d/halt S99halt
cd ../rc6.d
ln -s ../init.d/sysklogd K90sysklogd
ln -s ../init.d/sendsignals S80sendsignals
ln -s ../init.d/umountfs S90umountfs
ln -s ../init.d/reboot S99reboot
cd ../rcS.d
ln -s ../init.d/checkroot S05checkroot
ln -s ../init.d/mountfs S10mountfs
ln -s ../init./setclock S01setclock
cd /etc/rc2.d
ln -s ../init.d/sysklogd S03sysklogd
You only need to enter setclock in the chmod command and setclock in the ln command if you're on a PPC system. Otherwise pretend it's not there ;)