If the head gasket was blown you'd be seeing signs of oil and coolant mixing, I think the boil over and it burping itself explains your loss of coolant since that hasn't happened.
One thing you can do to encourage good burping is to wait for it to get nice and cool, take off the rad cap and then massage the upper rad hose, squeezing and releasing and all that. Should encourage any air in there to bubble out after a bit of work.
If that doesn't do anything we need to start diagnosing an overheat, it would be a really big help if you could pick up an infrared thermometer and take a reading from the thermostat housing next time it does this. That's the same place the factory sensor reads, so it should give you a pretty good idea of the state of things.
Jeeps typically overheat one of two ways:
A) Under any significant load
B) Only at low speeds (40-), or during frequent stops and such
In the first case, you've got an issue like a water pump with a rotted impeller not pushing coolant, a stuck closed thermostat, clogged radiator, etc.... Something with the coolant flow is what I'm getting at. The remaining thing to check here is probably the water pump, usually they start leaking slowly from the weep hole when they're bad because the seals typically fail before the impeller itself, but it's still possible and your flush and what not should have covered other issues pretty well, at least enough to change the behavior some. OH and the hoses themselves. If they get old and soft enough they can collapse under pressure and cut off flow.
In the second case, it's usually a bad mechanical fan clutch, the fan shroud or the e-fan not coming on when it should (by default, it runs any time the A/C is on, or when the temps top a certain threshold, something like 212 or 215, I can't remember). Basically something with getting air over the rad properly when you're not moving fast enough for that to happen on its own. sounds like you already replaced the mechanical fan clutch and have a switch on the e-fan, so this should be down to the fan shroud being attached properly unless you got a DoA clutch somehow.
It's always harder to diagnose on a forum, but hopefully I've given you a couple things you can do to diagnose this. Also: you'll probably want to replace the rad cap after multiple boil overs. They're cheap and it's a good policy. Plus an old one can fail to let a system self-burp properly before it reaches full boil over and forces the issue.
Lifted, Locked, Stiffened
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