The solution is to change directory within the script. In my case, the user is mynodeapp and the node files are in the users directory (/home/mynodeapp/).
script
chdir /home/mynodeapp/
echo $$ > /var/run/mynodeapp.pid
exec sudo -u mynodeapp node server.js >> /var/log/mynodeapp.sys.log 2>&1
end script
I have yet to find out what $$ means on the echo line or 2>&1. Maybe somebody could chime in with this if they know!