Random Misfire Help Needed

Ty07allstar

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03 Protege ES
I have a 2003 Protege ES 5 speed. About 6 months ago I got a CEL for a random cylinder misfire. I replaced the coils, packs, and plugs and the problem went away. The other day my car started to stutter and misfire real bad then it went away. This is what it did before and it gradually got worse. The light hasn't come on yet but I know it's going to. The only thing done to the engine is the MP3 ECU. I run Premium fuel like I am supposed to with the new ECU. Do you think that putting the stock plugs could be causing the engine to misfire with the different ECU and fuel? Hopefully somebody can help. Thanks
 
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