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Hello guys. I have a 97 wrangler with a 2.5 liter that I replaced with a new crate engine and now has 20,000 miles on it. Everything engine wise was replaced at the same time. It is not a daily driver so it sits for weeks. I drove it two days ago and suddenly it started misfiring to the point it would backfire out the intake. I have been trough the plugs and wire. Distributer looks fine with no cracks. It will not misfire until the engine is at running temp and never misfires at an idle. It will only misfire when it's in a pull. I do not believe it's a fuel problem not do I believe it's water in the engine. I was thinking crank sensor but am confused as to why it only misfires when warm and only when it's actually being driven not at all in an idle. The check engine light is on but only shows codes 12, 31, 65. No real help. Any ideas
 

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I'd try to run a fuel stabilizer/water remover through it and see if it helps seeing how you state its sitting for weeks.
Back fire in intake usually 1 of 2 things, cat or exhaust clogging not letting flow through. Or. A timing issue.
Since the engine is new, I am guessing the exhaust is not. Remove the 02 sensor before the cat, it will be loud, but run it and see if the back fire stops. if it does- there ya go. Cat time.
 
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