Might be a good idea to check your fuel pressure. A clogged filter isn't the only cause for reduced fuel pressure, the pump and regulator could be to blame. If your motor is getting the fuel it needs, giving the spark it needs, then suspect something on the control end. PCM, Cam sensor, Crank sensor, etc... I would probably check the cam sensor, though. Take it off, clean it, and RTV it back into place. The gasket for it isn't so hot, if ya know what I mean...
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