Alright...what we need to do first is clear the check engine lamp. Than drive the car around for a day or two and see if the lamp returns. if so, we can get the codes read again at AutoZone and see if all the code return. i don't believe they will. These are common for coils, spark plugs are due at 100k, and the Knock Sensor code P0325 may be fictitious, unless it truly returns. If we get a missfire code on just one cylinder, you may want to install a used coil on that cylinder and see if the missfire goes away. When you purchase 8 new coils, there's a chance you may have gotten one bad one and it is now causing the missfire. So infact, you may have repaired the problem and created another. I'll explain how to clear the lamp manually in just a bit.
Let's focus on some other possibly causes of the rough idle/missfire. Other than the coils and boots, these are common to have faulty Crankcase Valves. On the back of the intake manifold is a valve that controls the negative crankcase pressure...it leaks internally and causes an internal vacuum leak. The most common symptom is a rough idle. Sometimes you can remove the oil cap with the engine running and hear a loud sucking noise, which will further condemn it; but not always. There is a special tool we use to measure the vacuum in the engine crankcase...to pinpoint this correctly. The valve isn't too costly, but the intake plenum comes off to replace it, about a $500 job at the dealer.
Another common failure that causes a rough idle/nissfire is the MAF (Mass Airflow Sensor) The sensor, is mounted to the air cleaner box and commonly sets a P0101, P0100, P0102, or P0171 and p0174 codes...but in the beginning stages of the failure, it can cause a rough idle and not set any codes. We should hold off on the MAF replacement, until all the other avenues are verified. The sensor is easy to replace, but the cost is around $350.
Have you replaced the fuel filter yet? If the filter is partially plugged, it will cause multiple lean misfires, rough idle, and lack of power. If it has never been replaced or not in the last 35k miles, you should get that out of the way.
If the codes do not return, and the rough idle remains, you may have worn engine mounts, which typical fail between 100k-150k. To verify this, you can place a floor jack under the oil pan while the engine is running...jack it up slightly to take the weight off the mounts...if the rough idle smooths out...this was just an engine mount concern.
Now, to clear the check engine lamp, you'll disconnect both battery cables. While they're still disconnected from the battery...touch them together for 20 seconds. Since the cables don't reach each other, you can use a large guage wire to connect them together. When you do this, you discharge the PCM (Powertrain Control Module) capacitor, which in turn clears the PCM memory. This is known as a PCM reset. Once the lamp is cleared, the car needs to be driven for about 2-5 miles to allow the module(s) to relearn the adaptives, therefore we cannot account for any rough idle, sifting concerns or such until this period is over. If the lamp comes back soon after this reset, than the problem is considered "hard" and we need another scan to find which codes were set. Also, ask AutoZone if they have a code reader to rent, if not, you may want to purchase one from an autoparts store or eBay for around $75 (sometimes less); it will be helpful if you plan to work on this car yourself.