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I am assuming the boat was serviced and/or running fine this spring?

When was your first tank of E10 fuel? How much of E-10 is in the tank and how old is it. Did you add any type of fuel conditioner to the tank when fueling?

Without anyone giving you better advice, I would rule out the tank and lines by buying and rigging up a small portable tank. Just run it to the port feeding the separator filter.

Regarding ethanol, I have read:

The ethanol in E-10 blended gasoline is, by it's nature, a solvent. It will clean grime. minerals and other material in your tank and lines. This may be what you are seeing in the filter.

If your fuel fill or feed lines are not alcohol-resistant (stamped on the hose) the ethanol can do damage to them. I would wonder about the gas lines on the engine too.

E- 10 blended fuel does not absorb as much water as straight gas. When it reaches it's absorption limit, phase separation occurs. There are 3 phases (not 2 as with straight gas). The three phases are water, ethanol (slightly altered) and gas (slightly altered).

With straight gas, the water separates and the gas is fine. With E-10, the gasoline part is modified and not good to use.

See this lFAQ page by Mercury