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I'm not familiar with Honda but I would reasonably suspect that the flashing MIL after EOC is caused by an ECM conflict of seeing vehicle speed sensor input and no input from the cam sensor or crankshaft sensor.
If the jerking is caused by misfire, two things can happen. The camshaft position sensor will command retarded ignition timing, and the 02 sensors will command lean as they are in a HC rich atmosphere.
When it is jerking, look at the short term fuel trim (stft). A negative number indicates a rich fuel mixture and a positive number in excess of 10 indicates a lean condition. These numbers would be very useful to know to make an accurate diagnosis
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