My Crown vic shakes at idle but doesn't do it.

The Engine Computer detected a problem, set a diagnostic fault code, and since the problem could have an adverse affect on emissions, it turned on the Check Engine light. A flashing light is the most serious and it means stop the engine immediately. Too much unburned fuel is going into the exhaust system and is going to overheat one of the catalytic converters. That will become real expensive real quickly.

You're describing a misfire that results in the shaking engine. With a misfire the unburned fuel and air go into the exhaust system where it's burned in the catalytic converter leading to the overheating. The cause could be as simple as spark plugs and wires that were ignored too long.

Yup, your engine uses a "coil-on-plug" ignition system. On '96 and newer vehicles the Engine Computer will detect which cylinder is misfiring and set the appropriate diagnostic fault code and turn on the Check Engine light. Many auto parts stores will read engine codes for you for free. If you get one that says, "cylinder 2 misfire", for example, switch the coil from cylinder 2 with one of the other ones, ... Lets say cylinder 6. Check the codes again later and if there's a code for cylinder 6 misfire, you can suspect the coil. If the code is still for cylinder 2, you know it's caused by something you didn't move or change. That means the spark plug or injector.

That is not true. Over half of the fault codes do not result in the light turning on. The only thing you can know for sure is that when the light is on, at least one of the code(s) COULD have an adverse affect on emissions.

There's three things I can think of that might apply to what you were told. The first is the person with the code reader could be misinformed about its use. His job is to sell parts. There's a very good chance he never was a mechanic and has no training in that area. He might think there is no code if the light is off. The fact is there can be codes because they are stored in the computer until someone disconnects a battery cable, or in many cases the problem does not occur again within a certain number of engine starts; then the code erases automatically. If your light was on recently, there IS a code stored in the computer.

Some cars do not set a code the instant the Check Engine light turns on. On Chrysler products you can know for certain there is a stored code once the light turned on, even for a brief instant. GM products use what they refer to as "pending codes". The computer hasn't seen a problem act up long enough or for enough times to warrant setting a code. It's keeping a closer eye on some condition and sets the appropriate pending code. What's frustrating and confusing is they turn the Check Engine light on for those pending codes making you think there's a problem when there may not be. Many code readers, as I understand it, do not read pending codes. THAT would be a case where the guy was right, ... You need to read codes when the light is on. But that still doesn't mean there are no codes currently in memory. Too many people take their knowledge of GM products and apply it to all car brands. That could be what happened here.

It is also possible the code reader he was using has some type of programming that requires the light to be on currently, but that is suspect because the manufacturers of those readers know the light won't always be on. At any rate, I'd try a different parts store first. If they can't help, then you'll need to find a mechanic with a full scanner. Simple code readers used by parts stores cost from 50 bucks to a few hundred, and that's all they do is display the numbers. Scanners used by mechanics cost up to more than $6000.00 and display live sensor data and current operating conditions related to every computer on the car, and we can talk back and forth to the car and command systems to turn on and off for diagnostic testing. They are WAY more sophisticated than a code reader. Most code readers also only access the Engine Computers, not the dozens of other computers on the car. Most shops have to update their scanners a few times per year and that is also expensive. They have to charge you to use that equipment to help cover the costs.

To add to the operation of the Check Engine light, you can get an idea of the seriousness of the problem that was detected by how the light acts:

1) If the problem is minor AND it can't affect emissions, the light will never turn on but the code will still be in memory.

2) The light will turn on if the problem is more severe and / or it can cause emissions to increase. If it is an intermittent problem, it will turn off when the problem goes away.

3) If the problem is more serious, the light will turn on as before but if it's intermittent and goes away, the light will remain "latched" on until you stop and restart the engine. Then the light will stay off until the problem is detected again.

4) Still more serious, ... Even if the problem stops occurring completely at this time, the light will remain latched on even after you restart the engine. The problem is gone; the engine runs fine, the code stays in memory, and the light is always on.

5) This is the most serious when the light starts flashing. For some reason there is too much unburned fuel going into the exhaust system and the catalytic converter is going to overheat and melt. Besides being a fire hazard, That will destroy the effectiveness of the catalyst requiring its replacement, which is expensive.

It's important to note too that number 4 refers to an INTERMITTENT problem that is not currently acting up. The light will also be on all the time for numbers 2 and 3 when it's a constantly-occurring problem.

Can't help with that one. Any chance the filter was installed backward and a check valve is blocking fuel flow? You may want to use a gauge to measure fuel pressure to see if that is in fact the problem.