Rough Running XJ

My buddy bought an early 1996 XJ with a 4.0 and AW4. She starts and runs decent but here are the gremlins I'm chasing. I'm looking for some suggestions on what to start replacing.

The car kept throwing multiple misfire codes so we swapped in some new plugs, wires, rotor, and cap. (this helped but did not totally solve the problem.) He currently has no rear O2 sensor hooked up. It is gone and may have been gone for a while from the previous owner. And we are getting throttle position sensor error codes occasionally. It runs rough at idle and decent at highway speeds but it seems to buck a little like it is misfiring while at highway speeds. We have tried cleaning out the IAC and such. I think we are getting some improvement just not any quamtum leaps in improved performance. I did notice while climbing back into his car (the carpet has been removed) the floor over the cat was hot enough to cause 1st degree burns on my hands. This has me thinking we may have a plugged up cat but I'm not sure how it would run better at high RPM if it is plugged up ? ? ? ?. Any ideas what else I should check out?

THE CAT IS THE PROBLEM!!!!!

REPLACE THE CAT OR TAKE IT OFF AND HOLLOW THE INSIDE OUT THEN PUT BACK ON.

A stopped up cat will kill the way an engine runs it will make the engine loss power, run hot, and make it drink gas.

Also clean the throttle body, IAC, and Egr valve realy good. Use a tooth brush or small soft brass wire brush(Best) and throttle body cleaner.

Yeah It might be the CAT I guess but wouldn't that thing run worse the faster you try to go? I got no problem playing cat doctor and hollowing it out but what does that do to the downstream o2 readings? By the way where is the EGR valve on a 1996 ? ? ?

Dam I have allmost the same kind of problem. Just notice once in awile it will miss, out of now where and then run fine What the he11. its not all the time just here and there and at any RPM range (at a red light, down the hwy, just takeing off from a red light) When i bought the jeep the guy said it just had a tuneup done and every thing looks new but you know how that is!!!!!