67 A/C heater box rebuild and install help

Looks like you have the correct foam seal there ? Its not really a weather tight seal. It should fill the void though.
That rod has a predertmined length and thread length so you cant over tighten the nut right through the bottom of the box.
I suppose you could add a couple of flat washers underneath the box.Then again that how they get broken.
Can you feel the raised rim around the cowl opening and where the rod hooks ?
Is it rusted away ?