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I know there are quite a few posts on this on here but I can't find one that's really close to my situation. So here we go.

I have an 04 Intrepid 2.7. A while back I noticed it was lagging on acceleration for the first bit but would catch and fly with no problems at speed. Then it started an issue of when I was stopped, in gear with foot on the brake it would shudder now and then. Idle fine, shake, idle fine, etc. It finally threw a code of cylinder 2 misfire. I replaced all the plugs from some I had on the shelf for a while and it ran great for a week. It started all over again so I bought brand new plugs (champions) and put all those in. Again, a week later it was doing it again. So this time I bought a new plug and new coil and placed them in the number 2 cylinder. It worked great, ran better than it ever has.. for 30 minutes. Now it shudders at the stop with brake on but in neutral it runs smooth. It also now throws the codes for cylinder 5 misfire and general misfire. Also it now after getting warm will hesitate, chug and feel like it pulls backward a bit when I am going 40 mph +. Not as bad over 50 mph but between 40-45 you really feel it. After the initial hesitation and before 40 mph it runs fine.

I have replaced the cam shaft position censor, timing belt/chain (shop did that when water pump was replaced), coil on #2 plugs, wires look fine but I am not a trained mechanic, sylenoid on the tranny, tranny flush, sensors on the tranny, sending and receiving units on the tranny, radiator, and fuel line from top of engine back to the tank. Also replaced all belts. I know some of that has nothing to do with the issue probably but I want to cover all my bases. Any help would be greatly appreciated. I am about to go change the crankshaft sensor and intake gaskets, perhaps even the wires that go to the coils now and hope. Thanks again for any and all help.
 

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You could try swapping some of the likely suspects with cylinders that don't report misfires, e.g. coil and injector to the other side. (But don't disconnect the battery.) If the misfire follows to the cylinder where #5 came from then you can replace the part you moved. However, if the misfire stays on #5, you might have mechanical issues which a compression test might reveal.

If all tests don't yield any results, you may have a wiring issue or PCM fault.
 

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or you could of gotten a tank full of crappy fuel,

always start with the basics,, fuel, spark,, compression,
 

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or you could of gotten a tank full of crappy fuel,

always start with the basics,, fuel, spark,, compression,
That happened to me two summers ago with the old Caravan (my daily driver before I bought the Intrepid). For some reason, I was convinced it was an electrical issue, so I had the thing towed home and spent a few hours with a multimeter and wiring diagram. Then I checked the spark and pulled off the upper intake plenum and watched the injectors firing as it cranked over.

It had "coincidentally" started running like crap and eventually died right after I filled up the gas tank. Turns out 5 of the 16 gallons I had pumped were water. Real nice. The fuel pump "coincidentally" died a week later. I "coincidentally" haven't been to that gas station since.
 
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