Help with TJ going into limp mode

When was the last time you replaced the transmission filter? Mine sat for a while and a lot contaminants settled and made the fluid in the bottom of the pan blacker than bad oil after an oil change (tranny fluid looked good when checked normally, though). That's what fixed mine. Still shifting great for me.
 
The only other thing I could advise you on is the AIP sensor. They have them on Amazon pretty regularly. That was the only solution I had.

I’d also say it’s very unlikely that a new 4.0 would fix the issue since the problems aren’t with the engine itself.

You could always look for a junkyard with a 05-06 Tj 4.0 and take that sensor.

Hope it helps!
 
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Has anyone made progress on this yet? I've had similar issues, and continue to fight with it. I ended up replacing my 4.0, when I lost a cylinder, with a Golen 4.6 Stroker. The motor was swapped a few times, and rebuilt by Golen. I have been fighting, right along, the engine going into limp mode (hard starts, low redline, etc..), and throwing all the fun camshaft codes (p0344, p0340, p0016, etc..). It seems to do it during specific conditions..if I start it up, and drive off (without letting it come up to operating temp), in colder, sub 40° outside temps.. Also, seems to if I get heavy on the throttle. In all cases, I can turn the Jeep off and back non again (even just with the clutch in, and costing down the road)..and it's no longer in limp mode, though the codes are still thrown. I've replace the opda, crank sensor, and camshaft sensors with OEM MOPAR (when they were still available), checked the wiring, re-timed the engine...just at a loss. The only thing I can think of, is (and it may be a stretch) a bad camshaft. Maybe it's got a low spot, that causes read issues when it's cold, or torqued...but, that could be attributed to a bad wire too, I suppose. Any input would help.
 
Did this ever get solved i am having the exact same problems and done all the exact same things pcm opda ensured at Tdc engine and opda I have a P0016 I'm at the point of needing a cam crank re learn
 
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Here is how to fix the 0016 code-


Here is how to fix the 0016 code-


Awesome ya I'm waiting on a shop to do it for me they're booked out I have an Apollo d9 snap on tool and it won't allow me to "re learn l" it it's grey and un selectable when all the other options are selectable and black anyways yes I have the wrangler fix pcm I have crown opda everything's at Tdc I also have oem cam and crank sensors the jeep starts rough idles won't rev past 2k gas very slim throttle response I've also pulled exhaust to make sure cats aren't plugged it's gotta be the cam crank re learned out of synch driving me mad
 
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