We replaced the motor in my jeep with another 4.0 and after hooking everything up there is another 3 pin plug on the wiring harness that didn't get used. It's up near the fire wall. We thought at first it was for the CPS but that plugs directly into a wire going into the firewall. We are confused about this.

 

3 pin plug with only 2 wires in it?

If so, it could be the old CPS connector which shoulda been clipped off when the newer style "direct to ECU" modification was done.

 

To my knowledge since owning the jeep since 2011, no modification has been done to it. When we unhooked the wiring harness to pull the motor, my buddy doesn't remember anything hooked to it. I'm looking through old pics I have trying to see if it was ever hooked up.

 

i zoomed in on this pic and if that's the plug, it looks to be connected to something but there isn't anything there now to connect it to. Did the EGR have a connector on it or just vacuum lines.

 

That's my point.
Back in the 80s and 90s, the factory had a CPS wiring mod, performed by the dealer per a TSB as you describe on your Jeep.
Part of the mod was to cut off the old CPS connector when finished. Many times it was overlooked.

 

What color are the wires? Here's a pic of the CPS connector on my '88 (yes, it's still there). It's the only 3 pin connector like it back there.

Note the wiring colors.

 

Okay, I misread. I thought you were saying the CPS harness went into the firewall. Anyway, that doesn't matter at this point.
Does it run fine?
What color are the wires on the mystery connector? Same as CPS by chance?

 

That's what I read too.

So where do they splice in the CPS for the TSB? On the "other side" of the C101? Like bypassing the C101 but only with the CPS harness? Guess that could explain why the connector is still there as you suggested.

 

Yes.

https://www.tsbsearch.com/Jeep/18-51-88

I have it saved on my computer somewhere.

And, there's an easy way, if you don't wanna do the C101 delete, to mimic the results of the TSB.