2003 cavalier missing on cylinder 2

Is the PCM controlling the coil's ? You have B+ voltage at the dark green with orange trace wire at the coil pack ? The other two wire's go to the PCM - the PCM has transistor's that supply a ground to those two wire's when signal from crank sensor is seen . Opens an closes to build up voltage an to release a spark . You can test this control with a test light . Video's on youtube.

Wires !!!!!!!!!
And Are The New Plugs Gapped Properly

You visually checked for spark and there was none? #3 and #4 show to be on same coil, each coil fires two plugs. Battery has a full charge? The red wire at coil pack is voltage, it has good voltage? Any applicable trouble codes?
The yellow wires with different tracer colors are grounds controlled by the pcm, one ground for each coil. Did you check voltage on ground wire engine cranking? I can't rule out a faulty coil driver in pcm. It's possible your old coil pack damaged the coil driver in pcm? If that is the problem, hope it didn't hurt the new coil pack.

Diagnostic Test Code (DTC) P0316 means that a cylinder misfire was detected within the first 1000 revolutions of the engine crankshaft after engine startup. This code will always be stored at the same time with freeze frame data and a fault code for the offending cylinder.
This is where DTC P0305 comes in.
This code means that cylinder #5 is the cylinder that is causing the misfire.
Coils and plugs are only two of the many possible reasons for a cylinder misfire.
The possible reasons for both of these codes are:
> Damaged crankshaft position sensor
> Ignition system (Primary or Secondary)
> Faulty fuel injector or fuel injector control circuit
> Poor fuel quality (will usually cause MULTIPLE cylinder misfire codes)
> Base engine faults (burned valves, low compression, damaged lifters or cam, blown head gasket, etc.)
> Damaged/malfunctioning PCM

NOTE: The LEAST LIKELY cause is the PCM. A damaged Crankshaft Position Sensor will usually cause problems on ALL cylinders, not a single cylinder, however it IS possible if the sensing ring is damaged.

Do you have a simple miss on 2 cylinders? If so, you might be looking at a fuel injection problem, specificially a computer problem not firing the fuel injectors for the two cylinders in question.

I would investigate that route.

Could also be a module for the coil packs, that the coil packs sit on.

The coil pack unit's circuit #3 drives plugs #3 and #6 directly from the PCM. If the cam sensor was defective, it should not fire any plugs. Suspect bad wiring from the PCM to the coil pack, the PCM unit itself, or a segment of the camshaft position sensor surface has lost magnetism causing missing signal to the PCM. An oscilloscope is the best test instrument for chasing down a missing pulse problem. The missing timing signal also explains why the PCM would report a 'bad camshaft sensor'. Hope this helps!

could bea few things. Excessive moisure, low fuel pressure, Faulty coil pack, spark plugs gap or wires. Have you changed any of those at all? Let me know

1. Note: Electronic Ignition engine timing is entirely controlled by the PCM. Electronic Ignition engine timing is NOT adjustable. Do not attempt to check base timing. You will receive false readings.
   

The CKP sensor is used to indicate crankshaft position and speed by sensing a missing tooth on a pulse wheel mounted to the crankshaft. The CMP sensor is used by the COP Integrated EI System to identify top dead center of compression of cylinder 1 to synchronize the firing of the individual coils.

1. The PCM uses the CKP signal to calculate a spark target and then fires the coil pack(s) to that target shown in Figure 51. The PCM uses the CMP sensor not shown in Figure 51 on COP Integrated EI Systems to identify top dead center of compression of cylinder 1 to synchronize the firing of the individual coils.

1. The coils and coil packs receive their signal from the PCM to fire at a calculated spark target. Each coil within the pack fires two spark plugs at the same time. The plugs are paired so that as one fires during the compression stroke the other fires during the exhaust stroke. The next time the coil is fired the situation is reversed. The COP system fires only one spark plug per coil and only on the compression stroke.
   
   The PCM acts as an electronic switch to ground in the coil primary circuit. When the switch is closed, battery positive voltage (B+) applied to the coil primary circuit builds a magnetic field around the primary coil. When the switch opens, the power is interrupted and the primary field collapses inducing the high voltage in the secondary coil windings and the spark plug is fired. A kickback voltage spike occurs when the primary field collapses. The PCM uses this voltage spike to generate an Ignition Diagnostic Monitor (IDM) signal. IDM communicates information by pulsewidth modulation in the PCM.

1. The PCM processes the CKP signal and uses it to drive the tachometer as the Clean Tach Out (CTO) signal.
   

2.5L V6

The ignition system consists of an ignition coil, spark plug wires and spark plugs.
The crankshaft position sensor signal is the basis for ignition timing calculations. The alternating voltage signal from the crankshaft position sensor is digitized by a pulse former within the powertrain control module. This digitized signal is then used to position the closing time of the primary circuit of the ignition coil.
Ignition timing is determined by the powertrain control module in response to engine operating conditions based on stored data tables or maps. Once ignition timing has been determined, the powertrain control module interrupts the current to the primary circuit of the ignition coil thus triggering the ignition spark which is supplied to the cylinders through the spark plug wires and spark plugs.
The ignition coils are triggered by the powertrain control module in pairs (cylinders 1 and 5, cylinders 4 and 3 and cylinders 2 and 6) sending one ignition spark to the firing cylinder and one ignition spark to the corresponding cylinder on the exhaust stroke. This ensures that any unburnt fuel residues remaining in the cylinder on the exhaust stroke are re - ignited to provide cleaner exhaust emissions.
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2.0L 4 cynder

The ignition system consists of an ignition coil, spark plug wires and spark plugs.
The crankshaft position sensor signal is the basis for ignition timing calculations. The alternating voltage signal from the crankshaft position sensor is digitized by the powertrain control module. This digitized signal is then used to position the closing time of the primary circuit of the ignition coil.
Ignition angle is determined by the powertrain control module in response to engine operating conditions. Once ignition angle has been determined, the powertrain control module interrupts the current to the primary circuit of the ignition coil thus triggering the ignition spark which is supplied to the cylinders through the spark plug wires and spark plugs.
The ignition coils are triggered by the powertrain control module in pairs (cylinders 1 and 4 and cylinders 3 and 2) sending one ignition spark to the firing cylinder and one ignition spark to the corresponding cylinder on the exhaust stroke. This make sures that any unburnt fuel residues remaining in the cylinder on the exhaust stroke are re - ignited to provide cleaner exhaust emissions.
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Integrated Electronic Ignition System The Integrated Electronic Ignition (EI) System consists of a crankshaft position (CKP) sensor, coil pack(s), connecting wiring, and PCM. The Coil On Plug (COP) Integrated EI System uses a separate coil for each spark plug and each coil is mounted directly onto the plug. The COP Integrated EI System eliminates the need for spark plug wires but does require input from the camshaft position (CMP) sensor.
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It sounds like this could be a common problem - usually this is caused by the crank sensor going out/bad. The sensor is mounted to the timing cover on the front of the engine.
The crankshaft sensor provides both engine speed and crankshaft position signals to the ECM. The sensor is a variable reluctance device, consisting of a bobbin coil with a magnetic core. The resistance of the coil is approximately 1.35 kilo ohms . The steel teeth on the crankshaft timing ring are used as a rotor. As the rotor teeth pass by the crankshaft sensor, pulses are generated.

The rotor has 60 tooth positions set at 6° intervals with three teeth missing. The gaps identify the TDC position of the 6 cylinders during one complete engine cycle (two crankshaft revolutions). The rotor thus provides both engine speed and crankshaft position information to the ECM. The missing pulses identify crankshaft position. Each tooth pulse after the missing pulse represents 6° of crankshaft rotation. Thus the frequency of the toothed pulses are a measure of engine speed.

Im surprised that didn't fix it. On the Quad4 engine its usually a cracked coil housing.
Have you checked:

• fuel injectors / fuel pressure
• coolant temp sensor
• compression - to check for bad head gasket
• ignition control module
• EGR system - make sure the valve isn't stuck
• crank position sensor.

The crankshaft position system variation compensating values are stored in the PCM non-volatile memory after a learn procedure has been performed. If the actual crankshaft position system variation is not within the crankshaft position system variation compensating values stored in the PCM, DTC P0300 may set.