I used a spacer.
I also re-used my old throttle linkage, cut up a piece of the Offy linkage, added it to the old linkage and used it. I did this because I'm running an auto and needed to hook up the kick down linkage.
As to sealing up the plugs in the bottom: I used epoxy then painted my intake to match my engine. I also used a file to file off the logo so it stands out. Came out nice.
For heat:
I tee-d off at the firewall using brass fittings from Lowes. Tried plastic and they broke. Couldn't get a good seal. The brass lets you crank down hard.
Upskirt shot:
(note my handy firing order diagram in sharpie on my bench...)
You asked about the two holes. One is for the bracket that holds the throttle cable. Re-used your old one. The other hole is for the brake booster. If you don't have one plug it.
For the heat plate I took a 1/4" steel plate, cut it up, drilled my holes, tapped it, put the brass fittings in, cut them off on the back side so they clear the guts of the intake, then used a piece of rubber to make a gasket to seal it all up. I also RTV'd both side of the rubber. Without the rubber it wouldn't seal.
