Can someone tell me what this is?

#3
hmmm, well besides a bootytastic rats nest of wire, vaccum lines, hose clamps, and other various fun stuff, it looks like something that hooks into the heater core. I'm not YJ smart, so I'm not sure what its called.
 
#5
Yes that definately looks EGR/emissions related. The bottom side probably hard pipes down to the collector on the manifold or back around the converters I would guess.
 
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