I could see some water being rain-driven past the companionway boards, but all the water seemed to be originating from the bilge. The carpets in both the aft cabin and main saloon were a little wet, but if the water was being forced bast the boards, I would have expected the berth, bulkheads, etc. would show signs of water ingress.Before I cleared the cockpit drains, I checked the cockpit drains where they pass through the engine room, and there was no indication that anything had leaked in there, or anyplace else under the cockpit. I don't think that the water was forced back through the waterlift muffler. I did find one of the 4" duct that runs from a clamshell vent into the engine room was out of position. It's normally straight down from the clamshell, then vertically next to the fuel tank. It was extended straight from the vent to about midline in the engine compartment, but I can't see how that much water could bet blown into a 4" vent. The stuffing box waas repacked last year with Goretex Virtually Dripless packing, and showed no signs of the water coming in there. I've been chasing and fixing small leaks on the cabintop and deck that had caused core damage, but most of the leaks have been fixed, and in any case, they were minor, just enough to damage the core as the PO was very lax on maintenance.
The charger is a Xantrex 10A dual-bank smart charger, and I don't know why it didn't start recharging the batteries once AC came back. The only electrical connection submerged was the automatic bilge switch, and that should be ok submerged. I'm pretty much perplexed by this, as I've had the boat for 5 years, and it has been through weather at least this bad, and never had much in the bilge. It's possible the wind was shoving the water in a different direction than usual, but it was an AWFUL lot of water, and I really can't see where it came in.
Thanks for the responses; any other ideas?