Hi bombadore23,
Welcome to the site. Can you describe the problem a little more. Is it missing under load? Does that sound like your problem?
A miss or rough idle is caused by a cylinder not firing. The most common cause is a spark plug lead. They will usually fail completely, causing a miss most noticeable at idle, or fail under load, meaning when the engine is working it will have a seemingly random misfire. So start with the spark plug leads. They are cheap and easy to do. Wouldnt hurt to do the spark plugs while you are there.
The coils produce the high voltage for the spark, and so can also be the problem. They are more reliable and more expensive, so your best off not worrying about them unless the leads dont fix your problem. Using a multimeter you can measure the resistance of the primary and secondary of the coils, its fairly easy to do. If it is an intermittent problem though, the coils will probably measure fine.
Worth checking error codes too, instructions are in the how-to section. - Start with this!
It could be the IAC valve too. That controls the idle. If that was playing up you may get an error code.
The engine could be flooding too. Check the fuel pressure regulator. There is a vacuum line coming off it. If there is fuel in the vacuum line the engine will flood.
Could also be a loose vacuum hose. Check for any deteriorated hoses or loose hoses, especially if you have been working around the engine recently.
Actually grab a gregorys manual if you dont already have one. They would have a better check list with instructions on checking each. Probably your best bet if your still having trouble.
Let us know how things go