I have an 87 2.5l TBI so it should be very similar. There are two temp sensors. The one for the gauge is at the back of the valve cover on the driverside next to a big bolt with a ground. The Coolant sensor is on the SIDE of the manifold next to and facing the brake booster. It's hard to see. It's kind of hard to tell from your pic but at the bottom where it is cut off that looks like the IAT sensor. That being said if you are right that the coolant sensor is in the IAT spot then the male connector shown in the pic would be for the acutal IAT sensor that goes there. That is just an assumption. There are a few things that connect in that general area (the IAT, CTS, TPS, etc.). I am little confused though because there are two sensor looking things in your pic going into the top of the manifold. The one with the weird wire and the one to the right next to the fuel line. I think I only have one (the IAT). I would have to go look though. I am not sure what you mean when you say the cts is hooked up and running to a box attached to the throttle body.
I also have that large connector shown in the pic along with several other unconnected pieces. I think they may be for parts I don't have for other model jeeps.
Even though it's fuel injected I have to press the pedal to start and hold it to maintain idle until it warms up. New fuel pump and injector didn't fix it. Mechanics couldn't figure it out. I thought it was the cts so I replaced it but the new one wouldn't thread all the way in. I left in a few days or so but nothing changed so I put the old one back in. The IAT was dirty so I cleaned it but the plastic housing/cage that goes around the little disc sensor disintigrated. I can't find a replacement. anywhere. So I just put it back in.