To find the ‘dead’ (misfiring) cylinder, you're gonna' do is to ‘short out’ two cylinders at a time.
And you're gonna' do this with two pieces of vacuum hose and a test light. By taking some very simple precautions, this test will give you a very, very accurate result that won't shock you or fry the coil pack that you're testing.
As you already know, each coil pack has two towers, therefore, you'll be testing both towers of one coil pack (one coil pack at a time of course), and this is what you'll need to do:
Choose the coil pack that you want to start with. It doesn't matter which one you start with, since you'll test them all.
Now, disconnect the two spark plug wires connected to it. Attach one piece of vacuum hose to the inside of the spark plug wire. This has to be a small piece of vacuum hose.
Once you've got the vacuum hose inserted into the spark plug wire, connect the wire back onto the coil pack tower. See the photo in the image viewer.
The next step is to do the same thing to the other spark plug wire.
When everything is set up and you're sure that the spark plug wires are not going to come unplugged from the vacuum hose (that's now tightly connected to the coil pack tower)... have your helper crank and start the engine.
The vacuum hoses will help in transmitting the spark to the spark plug wires without causing a misfire themselves.
Now, with your 12 Volt test light (and whose alligator clip MUST be grounded), touch one of the vacuum hoses (see photo 3 o f 3 in the image viewer).
What will happen is one of two things, either you will hear a drop in the RPMs or you won't. If you do have a tower that you short out and it DOES NOT produce a drop in RPMs... then this cylinder is dead (but more about this a little later).
A cylinder that is NOT dead and producing power, will cause a drop in RPMs when you short out its coil pack tower with the test light.
Repeat step 6 as many times as necessary on both coil towers, to make sure you do or you don't hear a drop in the engine's RPMs.
The next step is to do the same thing to the other spark plug wires.
Although the above instructions are pretty much self explanatory... let's take a look at what your results mean:
CASE 1: The engine RPMs dropped when you shorted the coil tower with the test light: This result confirms that that cylinder is NOT dead and working. More specifically, it means that the cylinder has good Compression, has fuel and spark and that it is NOT causing the misfire.
CASE 2: The engine RPMs DID NOT drop when you shorted the coil tower with the test light: This result confirms that that cylinder is dead. This dead cylinder will cause a rough idle/ misfire condition. You have found the cylinder that's misfiring.
Now, this test does not tell you the specific reason the cylinder is dead. This test just helps you to find which of the six is dead.
What you have to do now, is to troubleshoot the coil pack, spark plugs, engine compression, fuel injector... you get the idea.
“Remember, this hobby is supposed to be your therapy, not the reason you need therapy.”