Thanks for the comments. I will (hopefully) find out pretty soon how it works.

The manifold seems it will mostly close the gap (as in the last shot) and the Indy intake
is really just for my own education/to get it running and check it out.

I acquired it used and still glued together which gave me a good look at how the previous owner sealed it up.
The valley tray got a heavy bead, like 3/8, then the intake was installed on top of that
which squished it down, then they went over the bead with the underside with a fingertip or
similar. Who knows what heads or other parts they used, though.

It's kind of nice to be able to use the china wall bolts without fear of cracking anything.