That's a shame.
Do you know if the hull end of the vent hose has the desired upward "reverse trap" to greatly help keep water from outside where it belongs?
Have you rechecked the o-ring. The wrong size or wrong profile replacement O-ring may not allow the cap to fit just right with intended seal.
Normally the only places or way substantial water can get into fuel tanks is through the vent, through a leaky sender gasket if water can drain down from the sole to sit on tank top, pumped in from a bad supply , mistakenly added in to fuel tank instead of water tank,.... with slight amounts accumulated from condensation when low tank levels are maintained in humid wx. .
Hopefully you can rule out bad-someone's intentionally adding water to your fuel tank.
What kind of vent does the hull have? If common "clamshell", is it still pointed open-end diagonally down and somewhat aft with screen intact?
Is the port side of the boat positioned in the slip where there is more wave action , either directly on the beam or as bounce back from a bulkhead which can be quite foreful in storms?
Was any water found in the stbd tank?
IMO, solid rainwater should never get in through a proper hull vent fitting, though it ...might... be possible for some water to get into the round non-directional disc type vents if there is no reverse trap and hose water is inadvertantly directed toward it during washdown.
6 gallons ! That's a lot in your diesel tank, almost 5%. Has there been some water right along since 2/9 which you have been removing from the separator bowls or do you think this is something which occurred in great volume just recently?
Just wondering , do you regularly add biocide like Biobor in label-recommended amount to help combat algae/microbe formation in the fuel water boundary?