2000 Si flashing check engine light. Missfiring causes?

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Im new to Hondas and I recently got a pretty much stock 00 Si. Its got a lot of miles (18X,XXX,) but it was running great until this morning. I let it warm up properly and was just driving around normally, but then gave it a quick run through the gears when provoked by some jack ass in a dodge ram. Shortly after I noticed the engine was obviously misfiring. I took it to Advance Auto parts to read the now flashing Check engine light. It threw 1. Random missfire, 2. Ignition system missfire, 3. Down stream o2 sensor, and 4. Emission system control something or other. The last two have been on since I bought it do to an aftermarket cat back. I replaced the plugs (NGK R v-groove,) wires (replacement,) cap and rotor also stock replacement. While I was swapping them I found what I thought to be the problem in that the rotor had some of the plastic ribs broken off and sitting in the cap. BUT when I started it up and let it idle it is still shaking and the check engine light is still flashing. I also just changed the oil with Valvoline Max Life yesterday, its not leaking and the level is normal. ANY IDEAS? sorry so long just thought Id clear up some things I figured I'd be asked.
what did your old plugs look like? Im guessing you issue is caused by a vacuum leak or a fuel pressure issue, to fix your cat codes go to autozone and get spark plug extensions, they will come in a pack of 2 and you will screw you senconday o2 sensor into it and screw it back into your exhaust, this will pull the sensor out of the cat farther causeing it not to see as many hydro carbons caused by having a high flow cat.
The plugs looked pretty good. No buildup, nothing looked overheated. I would almost guess they were changed shortly before I bought it. I did some more searching and found people with similar problems saying they changed the IAC. Does this sound right? I remember when my friends Z16's IAC went out it sounded more like a cycle of air pressue surges and drops. Id rather not spend another $100 for no fix.
I have had miss fires before because of a very old or clogged fuel filter or Clogged injectors... Also the wires I once used sh** the bed on me along with my dizzy all in 1 day and it was causing major problems... just some other ideas, oh and 1 other thing, with that many miles how is ya fuel pressure threw the car along with oil????? mite be some problems there!
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