There's a spec in the service manual.

What's the gauge showing?

 

The air temp coming thru the heater vents has a lot to do with it's original temp coming into the heater core and it's velocity. I've found on extremely cold days, using a lower blower setting results in higher heater temps. The air has to have time for the heat to transfer from the core.

 

Couple things:
1) Did you 'back-flush' the heater core? Flush in the reverse direction of the normal coolant flow?
2) There are tons of very tiny passages inside. If 1/3 of them became plugged, then you'd lose a lot of cooling capacity ...especially if they were fins toward the center.
3) Are there any valves in the line which may not be opening?
4) I don't know 99's. Are there vent doors with electric actuators which may be faulty? Any vent doors not moving? Are your vent doors closing off like they should?
5) Heater core?? True story: On two occasions I had cars that didn't heat well. Same as you. A 'little' heat, but always cold. I removed the heater cores a couple times and filled with different solutions and let them 'boil out' for an hour. These were on vehicles where the heater core was pretty easy to remove, like in 15-20 minutes (not our Jeeps!!). I tried multiple agents and chemicals and the heater core was SO hot sitting on the ground, from the chemical reaction eating out the mineral deposits, you couldn't even touch it! I'd put it back in and not really get a whole lot more heat. It was annoying. So, after a couple attempts, I broke down and spent whatever it was for a new heater core. One was about $200 from the dealer. Bam! I had instant heat like crazy! This is a personal true story. Once the tiny passages become plugged up, it's exceptionally hard to get them unplugged. Even if you managed to get a few unplugged, for all the time and energy, better to buy a new heater core. Never EVER use regular tap water in your radiator (or any stop leak). Great way to ruin a heater core. Use filtered, purified, or distilled water (purified is best), or buy a pre-mixed anti-freeze solution.

6) On my Cherokee, the foam seals on the vent doors in the AC/Heater box have dry-rotted (from age) and are gone ...allowing colder outside air past the heater core. Doesn't matter how well the core is heating, cold air will neutralize the heat output. Wait till it get's to be 32* outside!! You can't see it though. I know b/c one time I saw a lot of foam blow out from the heater. That was the last day I had good heat. It's common on these Jeeps. I can't believe nobody makes a good seal kit for these rigs?? (or do they?)
7) On some vehicles, a low-heat situation can be a sign that the head gasket is failing. That's not as common on these iron 6's.
8) Thermostat - Of course this should be the first item to look at. Hit the thermostat housing area or head with a infra-red temp gun when it's up to speed. See what the temp is.

There are 8 ideas ideas for you....

 

Excellent list!

The 99 does NOT use that obnoxious Heater Control Valve that was used in 96 and earlier XJ's so it should be a straight shot from the core to the engine.
The blend door is definitely "on the table" as a possible issue.

 

Mine ran very cool during the summer and sometimes too cool for the winter.
Culprit was a busted t-stat.

Just sayin

 

having the mixture more coolant than water will also drop the temperature. Not sure what your temperature highs and lows are for the outside weather, but recommend 50/50 mix through most of the US. If you want it to get warmer, dilute the mixture and that will allow things to warm even further.

As a few folks mentioned, thermostat has a rating and of course the heater core itself has to be good. After determining both are good (you can boil a thermostat to test it, it will jump when it hits the temperature to open). After you determine what the thermostat temp rating is, (assuming all parts are working) the next biggest influence is the mixture itself, the fan and radiator size. Because you flushed and noticed a difference afterwards, I would suspect your old stuff was watered down more than what you are using now.

Hope that helps.

 

Do yourself a favor when you're done and DON'T use regular tap water in the radiator. Use FILTERED WATER. Hard water will eventually clog up your radiator and heater core.

 

After a flush the block is filled with tap water unless the drains are pulled, adding straight coolant to the radiator will probably result in a perfect 50/50 ratio. Adding more water to the system (of any type) will probably thin out the mix too much. Always use a tester to be sure.

 

 

Mine had no discernible heat at the vents last winter. I quit driving it in the morning (wife had treatments at 6am every morning and a cold ride was too much). In early November, I pulled the hoses and flushed the core both directions. The heat would work for maybe the next morning, then nothing. Last summer I had a water pump leak. I replaced it and immediately started having overheat problems. I had never had that before. Water pump did not cause the engine to overheat when it failed. I changed the thermostat (It was already new last winter). That didn't help so I changed the water pump again (I really couldn't see why an engine that never runs hot would suddenly start doing so for no reason). I test drove the XJ and thought it was fixed, but after 15 minutes it suddenly started heating up fast. I got some radiator flush and following package directions ran the flush for about 400 miles. I flushed the system, refilled with tap water and ran engine for 20 minutes and drained system, refilled with distilled water ran 20 min. and drained. I blew out the cooling system with compressed air. I then repeated the same procedure with distilled water a 2nd time. I then added 1/2 a gallon of concentrated antifreeze and then finished with 50-50 mix using distilled water. The few cool mornings we have had this month were no problem. Within 5 minutes of starting the engine we have to turn the temp control to a colder setting. Hope it lasts. By the way I am in the south so YMMV.