My check engine light was flashing all the time and there was a ticking noise.

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Took it to O'Reillys and had it scoped. Diagnosis showed a miss in number six. I replaced all the plugs, wires and #6 coil plus added an injector cleaner. Now the check engine light remains on and only flashes upon acceleration and higher RPM. The ticking noise is still there but subsides after vehicle warms. Is this a lifter problem? Could a miss cause transmission problems as I've replaced through AAMCO four times. The last time the transmission was replaced, the light remained off for less than 100 miles then started flashing on an uphill grade. HELP