Cylinder misfiring
 

My friend has a '96 960 with a '95 engine in it. It threw some codes yesterday after he had done some work on it, and the codes were misfiring in cylinders 1,3,5. We swapped some coils to check if they were the issue, and turns out the coils are still good. My friend then mentioned that when he had worked on the car, he had forgotten to disconnect the battery, and had caused sparks by contacting the alternator with his ratchet. With these two events being directly related to each other time-wise, what could have happened? Could the system have back-fed?

It sounds like one of the power stages is malfunctioning or the connector has come loose.

1, 3 and 5 point to it, there are two power stages, one for those cylinders and the other for the even numbered.

Check the connector, they are located under the throttle body, one forward, one aft of the bulbeous part of the intake.

DanR '94 964 368,000 miles (134,000 on the new engine)

Sorry to be blunt, but maybe your friend and electricity shouldn't mix. How can someone work with the coils and forgetting to disconnect the battery?

Have you checked the fuses? Do you have a Wiring Diagram?