2006 Pontiac Grand Prix engine misfire. V6 3.4L. The check engine light is on.
I replaced
spark plugs and new wire harness, tranny flush.
My check engine light is on. This started when I set my cruise one day and it started to chug
immediately so I shut cruise off and engine light was flashing then stayed on. So put it in computer
and it said cylinder 4 misfire so I changed all the plugs and wires and it continued to do it.

I took it to shop and got a tranny flush and had them check why engine light is on and they said it
was just a malfunction so they reset it and I left there and my car chugged and light came back on.

The chugging happens when I am gradually accelerating and my RPM gauge is right above the 2.
Not sure what's wrong any ideas?

An engine misfire under load like you describe is usually caused an
ignition system component. I
would assume you have a code P0300 or P0302.

Accelerating from speed puts a big load on the ignition system. Most common cause for this is the
spark plugs or plug wires.  Since you replaced them, that of course was not it.

Next you need to look closely at the ignition coil towers. If there is any corrosion, that would be the
cause of your misfire. See picture below. Also look for a crack between the towers.

If that checks out OK, then next would be to diagnose a possible
fuel injector problem. Either the #2
injector is not firing, is restricted, or has no signal. Using a test light to check for pulse signal is
needed. If it has pulse, then a flow test would need to be done. A restricted injector will usually only
cause a misfire at idle, but can also when accelerating.

If all this checks good, then another possibility that is not as common is a rocker arm coming loose.
This can happen if the lower intake manifold gaskets were replaced in the last few months. Improper
torque can lead to a rocker arm bolt coming loose from the cylinder head. This can also cause an
engine ticking noise.

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2006 Pontiac Grand Prix Misfire And Chugging
A good GM ignition coil makes engine run smooth and no hesitation.
Corroded GM engine ignition coil and spark plug wire causes misfire code p0300