I do keep the boat in a slip but use it on a weekly or bi-weekly basis. It has dual engines and both tanks were replaced 2 years ago. All fills replaced too. As for our fuel yeah im in CA so we have Ethanol so that sucks. We don't really "put away" Here since i crab in the winder and there is always something going on. This is just part of maintenance and thought it was interesting.
You did all the right things. I fought water in fuel problems for a number of years. Particularly early in the year when I too my boat South to Florida. I tried stabilizers. switched to running only ethanol-free fuel, installed O-rings on fuel fills (mine were non-existent). A few times I thought the stabilizer caused the water to appear. Got to the point where I went to Siera clear bowl fuel filters in place of the Yamah cans.
My "normal" start of Winter boating is to dump the fuel out of the filters, fill with new fuel, put them back up and run the boat (bouncy ride trying to get any water in suspension). Repeat later or next day. I was never able to pump the water out. This was the only way I found to clean the fuel up. It's a pain for my first few days in FL but my problem would go away.
I don't know where my water was coming from. I suspect fuel fill O-rings and phase separation when using ethanol fuel. It doesn't take much water to cause phase separation after which the 10% E10 ethanol and the 0.5% water will drop out of the fuel.
Good luck!
BoatUS: Phase separation occurs when ethanol in fuel absorbs water from the air, forming a second layer of ethanol–water sludge at the bottom of the tank. This happens because ethanol is
hygroscopic — it attracts and holds water — and can dissolve up to about
0.5% water by volume before the two phases separate
mobilemarina.co+1. In a 20‑gallon tank, that’s roughly 12 ounces of water. Marine environments, with high humidity and frequent temperature changes, accelerate this process