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I have had this same problem for about 4 months as well. I have a 99 se 5 speed. I noticed the problem before I put on my intake on. I thought it was bad gas but with the intake on you can hear it make a popping sound. It is only at about 3500 - 6 and only at WOT. It happens randomly. I talked to my mechanic and he said that it is one of my coil packs going. If you keep on the throttle while it is doing this hesitation the check engine light will blink but not stay on and the ECU doesn't store a code. I red a post a while ago from some who had the same problem and they eventually just gave in and bought 6 coil packs and the problem went away.
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