My driver side lower flap cover doesn't seem to sit correctly over the flap hinge humps of the fan housing. Does this look correct?

Those caps are different side to side, (wider/narrower) make sure you've got the correct one, can't quite see from your photo.

I just put mine on last night (with engine in car which makes it a little tricky). Second one may be off as shown by OP. Did not realize they at different on each side.

Once on correct side, which end facs the exchanger?

This is the one I have for the drivers side? Which way is forward?

Check the profile against the flange where the retaining bolts went through on the S-duct. The edges line up pretty well when they're on the correct sides.

There were originally cork or rubber gaskets in there as well. To my knowledge, these have been NLA for a good while.

--DD