I would pull the smog off and add the cowl plenum. NOBODY has the cowl plenum and NOBODY that ran a cowl plenum back in the day would ever keep the smog on there at the same time. Smog does not physically fit with the plenum box and it makes no sense from a performance standpoint to have them both on the car at the same time either. Also, it leaves the door open to a set of period correct headers if you desire that.
If you don't do that then the next best thing would be is to keep the smog on and for the cowl plenum to be loose in the trunk as it would have been delivered. You could make a case for that "as delivered" condition but that isn't as much fun if you ask me.
Pet peeve of mine - Z/28's with the cross ram and stock exhaust manifolds. Nobody would have done that back in the day either but you can see it now.
Hope this helps,
-Mark.