You need one small (3/16" I believe) line going to the fuel pressure regulator from the intake. You need a big line going from intake to the PCV valve. You also need a big line going from intake to the vacuum tree on your firewall. The throttle body line should go to the passenger side valve cover. The other valve cover should be plugged completely.
Where they actually connect to the intake doesn't really matter as long as what is connected is supposed to have uncontrolled vacuum.
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351W 89 Mustang GT Convertible