Since you want to execute the pre-start stanza as root and the start stanza as nobody you have to use `sudo`. Try it with that upstart job:
description "Tagger Version 2"
start on runlevel [2345]
stop on runlevel [!2345]
respawn
respawn limit 2 5
pre-start script
mkdir -p /run/lemmatization/Lemmatizer
chown nobody /run/lemmatization -R
end script
exec sudo -u nobody -g nogroup some_shell_skript.sh
As you see I removed the setuid/setgid part completely and used `sudo` instead to execute your script as another user.