| The "Air Injection Reaction" system, aka, "A.I.R." system has been removed. That's what the connector in your first picture is for,
The air conditioning has also been removed. May not be too pleasant during hot Chicago summer days. The solenoid in your third picture is the idle "kicker" solenoid, to bump up the RPMs when the AC is turned on. Since your AC isn't functional, no big deal. The solenoid is also activated by the ECM during certain deceleration conditions to reduce emissions, but it isn't something you'd notice as a "running like it should" thing. Go ahead and reconnect it, won't hurt anything either way.
The vacuum port capped of in the upper left corner of your third picture is for the stock air cleaner. The open element air cleaner on there now doesn't need it, so it should be capped off.
Some more pictures with the air cleaner removed would also help. Particularly pics of the front and passenger side. | 
