You need to put them in. They are a tighter fit and help the alignemnt of the ports better.
Seems like it would have been a little difficult getting it all back together without them. Or, well at least a bit more than with them.
2006 Mustang GT in Torch Red
C&L Intake, Evolution Performance Tune, Borla Axle Backs, Hurst Shifter, 4.10's, JBA Long Tubes, Prothane Engine Mounts, Steeda UDPs, FRPP Charge Motion Delete Plates
84 Bronco, 302 C6 on 32 10.50's