P0339 CKP sensor circuit intermittent
That's correct the procedure to replace the starter you remove the intake manifold which depends the transmission being a automatic or manual transmission., Here the intake is removed to replace the starter, the code you set and need resolved is for P0339, having a CKP being intermittent will set the rest of the misfire code that you have. Unfortunately the CKP sensor is not any where near where the starter is being replaced. So you have a different issue. Solve for P0339 and your back on the road again.
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