I am not sure about the vacuum line to nowhere, but have the same line in same area on my 91 4.0L. It might be a breather line to the trans? just a guess really.
As per the two wires with the eye terminals that you show in picture #1, I am pretty sure those are grounding wires. On my jeep I have these wires too, they were connected to the grounding stud that is on the 4.0 block on the passenger side. I'm not familiar with the 2.5L block but I bet there is a grounding stud somewhere on the passenger side. These might connect to that if its like the 4.0L. On our jeep these two wires lay on top of the negative cable that goes to the negative on the battery, all retained by a nut on the grounding stud. The stud on our jeep can be removed by a torx fitting, not sure the size as I was grabbing on size when we replaced all our cables this week. Try affixing both of those wires in picture one to the motor ground or chassis ground if your jeep doesn't have a motor grounding point.