Well, I ended up starting to replace the heater core this weekend. Got it halfway back together when I realized I needed to take it all back apart, so this will be sitting in my parent's garage for a few weeks before I will get another chance to work on it.
This is what the heater core looked like:
Have you verified the reading of the CTS with a multimeter? I know you said you replaced it with new, but ya never know. Does yours have the split sensors (one for computer, one for gauge cluster)?
Also, have you verified your coolant temp using an IR thermometer?
Have you checked the overflow bottle while it's running hot? Maybe it's boiling into the bottle, but not overfilling?
I have not verified the CTS at full operating temp yet. I have done a few tests as it is getting up to temp (Just didn't have the time when I was testing to get it up to temp), because as you said, you never know. It does have the split sensors.
I have not had a chance to get an IR thermometer to verify temps. No boiling inside of overflow bottle.
Just throwing this against the wall, but I'm assuming a Stant brand T-stat? I don't want to open Pandora's box in your thread, but I've used aftermarket and dealer-bought T-stats, and I've had better luck with the dealer 'stat, with the check valve ball, installed at 12 o'clock. Possibly the system is air-bound? Either that or there's a major clog somewhere? I've seen majorly clogged plenum chambers, usually leaves, that had prevented just about all airflow. How's your air volume? You mentioned heater hoses getting hot. Supply and return? Possibly is the return much cooler?
I'm going to give you a worst-case scenario. Seven years ago, I pulled the head off my '92, to replace some ticking lifters. Never had an overheating problem. As I was cleaning the head, I noticed the rearmost coolant passage, in the head and block, was just about completely clogged with dried, coked-up coolant, like green rock. I cleaned it out good, and after driving it awhile, noticed that the temp was noticeably cooler, and that winter, it was like, WOW. Turkey roasting hot! I'd hate to see anyone yank a head chasing a possible clog, but my accidentally finding this was pure luck. My guess is that with high operating temps and poor heat output, there's most likely a clog somewhere.
It is a Stant as I said, and I've had no problems with them in the past. I agree, dealer would be nice, but I haven't had any issues with Stant in my '99. I don't believe I have any air in the system, as it is the open loop and I've gone through a few cycles of warm up and cool down after installing the t-stat to get air out.
Both heater hoses become hot to the touch (not warm, but hot), and there is not a large difference between the two. There were no leafs or blockages at all in the HVAC box.
X2. I've read that Stants are the best, but I've had problems with them. The dealer tstat is generally the way to go. Cheap and easy. I would start there since it's the basis of operating temps.
You've pretty much got your grounds covered by replacing everything else. I was going to say heater valve, but...did you remove it? If not, work it in the opposite direction to see if you get heat (obvious input but maybe you overlooked it?).
As I said in my first post, the heater control valve has been removed since I replaced the water pump 2 years ago.
Your compression is not uniform in all cylinders. The 20 psi difference in 2 of your cylinders is pretty significant and will affect you mpg. Also what condition is your O2 sensor in? A worn or faulty O2 sensor can greatly affect mpg as well. Just because your check engine light is not on or there is no detected trouble code doesnt not mean the O2 is good.
Its not too significant, it is within spec according to my FSM. 20% variation, 150psi nominal, so 120 would be the lower limit. I was talking with another older car guy, and he didn't believe that compression would make that big of a difference.
o2 sensor was replaced a month or two ago with a Bosch unit. I put Bosch in my '99 last year and haven't had any issues with them.
Regarding the heat in the cab, Have you verified that the blend door is functioning properly?
The blend door does rotate from one position to another. When I had the box apart, I noticed that there was a corner that wasn't sealed completely due to worn and compressed foam. I added a few new strips of foam to the areas, but since I won't have this back together for a while, I might look into a new blend door.
I am going to call BS on this. I am currently getting 15mpg on my 98 XJ. It has 150, 150, 30, 30, 150, 140 as its compression readings. The head gasket between 3 and 4 is gone, you can feel air rush out of 3 when 4 compresses and vise versa. I have verified my odometer and measured the amount of gas used down to the hundredth of a gallon, using the same pump each time. No, I don't understand it either, but compression isn't THAT big a deal as long as they are all sufficient for a clean burn.
Mark, it sure sounds like something inside the hvac box or dash to me. I know you said the coolant hoses are nice and hot to the touch but have you checked with an IR thermometer? Just curious, I expect them to be at the right temp but you can never be sure.
I would suggest the O2 sensor but you already replaced that. Have you checked the MAP sensor?
Map sensor tested within spec, I forgot to mention that in my first post. Double checked this weekend. Vac hose was replaced when I did the CCV hoses.
Jesh, I just spend a 1/2 hour answering this post, hit post and got a BS

token expired error message, and now I need to start over, CHIT!!!:flamemad:
I hate when that happens
OK, first check the fresh air/recirculate air door under the passenger side dash, near the door, there is a spring loaded vacuum operated valve there that operates the door. Bad valve or no vacuum to the valve defaults to cold ass outside air!!!!!
Checked, works normally. Opens and closes according to selections on HVAC controls.
Check each spark plug for bad combustion on one cylinder. Check all the fuel injectors, for leaks, too clean, too dirty, oil, and so on cause of bad idle.....Check the fuel pump pressure too.
Fuel pressure tested within spec at the rail, confirmed the pressure regulator isn't leaking too. I will have to double check the injectors, I noticed that the opening below the throttle body inside of the air intake looked wet, but I had seafoamed recently so I couldn't be sure if it was gas or seafoam. I pulled the plugs in cylinders 1-3, when I get home later I'll post a picture of cylinder 1. 2 looked fine, 3 was a little dirtier than 2, but 1 had a few more deposits than the others.
You may have, a small exhaust - head gasket leak, pushing hot air into the coolant, which would not cause loss of coolant, would cause the odor as gas escapes the coolant overflow bottle, and the silicate-silicone in the coolant would ruin the O2 sensor. Test the O2 sensor, and it's electric heater, and power feed....See here:
http://ns2.naxja.org/forum/showthread.php?t=1012701&page=5
If I am right about a small head gasket leak, the gas can accumulate under the T-stat, under the Gauge temp sensor and in the heater core, and cause some of your problems.
Get an IR gauge and verify the temps under the hood. Check that the Gauge sensor is actually reporting the real temperatures!!!!
I have ran the engine with the radiator cap removed a few times in the past, and again this weekend, and I didn't see any bubbles coming out. Not dismissing that idea, just observation. It could just be accumulating like you said, so I didn't see it.
I'll have to test the sensor at some point, but I don't think this Jeep will be back together and running for a while.
Maybe a good point, there are actually 2 doors. Would the blend door allow air to by pass the heater core? I mentioned the other door, fresh air door, which was my problem once.
Both operated fine when I observed with the box apart.