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Is that a problem to have an alternator that is not being used for its capability
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No, its output will be based on demand. So no issue with having more amps available then demanded.
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I understand it is a lot bigger and the larger gauge wire is needed
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As noted, the alternators output is based on demand, so the load on the alt will not be any different then currently, until you upgrade the stereo. So you do not
need to upgrade the wire now, simply to get back on the water. But, it sounds like the alternator swap is going to require some modification to make it fit, so I would just go ahead and lay in a new larger ga cable from the alt's output post to where ever the original goes.
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There is a 50amp circuit breaker on the boat now, does that need to be upgraded??
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This breaker's load (current draw through it) will not change with the alternator upgrade