Pics loaded well.
I'm not sure where your very first one is located, so you may have to zoom out a bit on that one, but it looks like the coolant tube to me.
The 2 fittings at the throttle body are for coolant as well.
The 2 ports you have circled at the back of the intake are for the brake booster (bigger fitting... looks like you already have it hooked up), and then the next is just for whatever... personally I'd use it for the fuel pressure regulator, which brings me to my next point... it looks like your fuel rail is on backwards. Traditionally the fuel pressure regulator is on the firewall side, and your fuel return line goes on to the back of the fuel pressure regulator. There's also usually a barb/bulb fitting on the line where the fuel line goes on, as seen here:
The rest of the ports you've got that come directly out of the intake can be used for anything you need them for, or can be capped off.