You have a tough one there.
I still wouldn't rule out voltage regulation and getting too much voltage so I would check the terminals directly at the alternator with a meter.
Next, I wouldn't trust the supply and ground. I would run a new 14-ga B+ and ground to the battery direct and definitely verify that its to the same battery or switch post as any amplification. Also, check the amplifier ground.
If those steps don't produce anything then strip the HU of all speakers, remote controls, RCAs, illumumination, remote turn-on lead or other inter-connections. Power and ground only. See how it behaves then. If it works fine under those conditions then reinstate one connection at a time. I know its primitive but simple isolation and elimination generally works.
There is a small chance that the HU is damaged, whether water damage or other, and that it fails when the voltage crosses a certain threshold, even though that voltage is normal. Look for any signs of corrosion or a white residue on the source unit.
David
Earmark Marine
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