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The alternator normally has absolutely nothing to do with the fuel pump. However, since they are not too far apart, in the process of replacing the alternator, something could have hit the fuel pump and damaged it. So, while there is an extremely high probability the two are not connected, there is a possibility they are connected.

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Q: You replaced a bad alternator on a 99 wrangler. could that cause your fuel pump to go bad?
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