I have a 2001 dodge Dakota 3.9 liter i used a code reader and it says cylinder 3 misfire detected. The motor runs great and never sputters out or anything so i don’t know why it says this.

 

A misfire can range from a full no combustion event to a delayed combustion event. The softer ones you might not feel. Check the spark plug/wire to cylinder #3.

 

All wires and plugs were replaced a few thousand miles ago and as i stated, motor runs great and never has any issue so I think it’s something throwing it off. Also have a code for high voltage o2 bank 2 sensor 2.

 

New does not mean good. I had a plug on my 5.9 crack 1000 miles after installing it just recently. The o2 sensor code likely means a bad o2. It can also be caused by damaged wires feeding voltage into the hot wire of the sensor. Unplug it and use a voltmeter to test the resistance of the o2 sensor. If its no resistance then you have a failed o2. If it reports a proper value then you may have the damaged wire scenario. If you replace the o2 make sure to use OEM parts if you can get them. People tend to have issues with aftermarket o2 sensors for some reason.

 

How about the cap and rotor?

Think I would go after the O2 sensor first though, solve that problem, and the misfire may go away.

 

The point is is that it is not actually misfiring. It never sputters at all the motor is very solid the code is just on.

 

As I said before your not going to feel every misfire. Especially one that is consistent and fairly soft.

 

Yes as mentioned look at 02 sensors 1st. an you can also swithch plug wires an see if misfire code goes to another cylinder..
You can test the outputs an readings on 02 sensors while running ,with a good scanner also..

 

The magnum engines do not have "knock sensors". The misfire events are calculated by the PCM in two ways:

1. Based on the upstream O2 sensor readings in relevance to when a cylinder's exhaust valve opens. In your case, the PCM may be seeing a "rich" spike on the upstream every time the #3 cylinder exhaust valve opens.
2. Based on the time between signals from the crank position sensor. The PCM keeps track of how many microseconds occur between each window in the flexplate. In your case, the PCM may be seeing a consistent inconsistency with the timing of the windows just before and after the #3 spark event.

The hole pattern is 3 equally spaced sets of 3 holes spaced as follows:
2 holes 8.5 deg apart then one hole 47.3 deg after the previous. The holes are about 4.25 deg wide.
So there area total of 9 holes, 3 doubles and 3 singles

The firing order is 1-6-5-4-3-2

If memory serves correctly, the double holes are on cylinders 1, 3, and 5. The problem that I ran into was that a worn out sensor, or even a cheap "new" sensor, would hang on the double windows and throw a multiple misfire for that bank. Since you only have 1 misfiring right now, I don't think that's your problem, yet.