I have a 90 YJ w/ TBI 2.5L and recently have had a problem where it runs ok when it's cold, but when it reaches operating temp. it suddenly starts running rough, and bogs out when trying to throttle up. I put a new ECM in it and that seemed to help slightly, but still does it. I also smell fuel from the exhaust when I stop the engine. I just bought this used recently and am working the bugs out.
I am having the same exact problem with my 89 yj with a 4.2L inline 6.
I put it in the shop at my vo-tech for a month, and...
I went to drive it home and as soon as it heated up to normal operating temp, it started running around 600 or 500 (hundred) rpms. it was really low and you basically could not drive it. I was able to drive it back to the shop after it cooled down, because it did not heat back up until I was back at the shop.
I replaced the distributor, and I believe that fixed that problem, but it still would bog a little when you would step on it hard. So I replaced the Ignition Control Module (same thing as ECM?) with another I ICM from a junk yard which also seemed like it helped, although I think it might be going too(because the heat makes them go). The mech at my school cleaned out the carb, but did not use a rebuild kit (he tried to reuse a bunch of seals and such) so I think that it did not get done the right way.
I just gave my jeep a tune up (placed spark plugs, wires, and fuel filter) still does not run the right way. Also the spark plugs looked as though they were runn a little lean, but since I'm not a mech. I was going to take my plugs to a mech and have him look at them. So I think that the problem is still the carb., but because it only does it when it's hot it might also be my ICM from the junk yard.
Hope that helps you out. Please let me know if you have any questions, because I'm trying to fix my Jeep and I might be able to help you out more. Also if you figure it out, PLEASE let me know.
Thanks, Jon.
P.S. - Does TBI = Throttle Body Injection? If not what does it stand for, and is your YJ a carb? I also get a lot of fumes up in the cab.