I have a similar problem here are the key issues:
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1: Dash lights all flash on intermittantly
2: Alternator is fine, yet it outputs nothing to the battery.
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3: When engine bay fan is supposed to kick in, the warning light for it comes on and power is then outputted to the battery.
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A ground problem would be most obvious i think, however I have connected jump leads to multiple solid earth points and the problem remains.
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any ideas? Where should i look?