If your 42 engine room vents are like the vents on my 37, the rain would have to be really heavy and the wind really strong to get into the engine room. I've had a couple of times where seawater got through the vents, but those have been in situations of heavy spray. Think crossing Rosario with southerly wind gusting to 50 knots and sheets of spray covering the boat almost constantly. I spent two days in Ketchikan in August with 15-20 knots of wind on the beam and 10 inches (it was a wet summer!) of rain and didn't have any rain make it into the engine room.
If you've got fresh water in the bilge, have you double checked the whole domestic fresh water system for leaks? The sink and shower drains? Does the P&T valve on your water heater dump (or leak) into the bilge or through a hose overboard? Is there a path for water to run forward from the lazarette to the engine room? If you turn the pump off and leave the boat for a week, when you come back, does the pump cycle on immediately indicating loss of pressure in the system?
Deck hardware could also be the culprit. Sealants fail over time (17 years seems to be about the time on my boat) and all the deck hardware eventually needs rebedding. Could the water be coming from the rail or cleats? I supposed the sealant around the engine room vents could also be a source of leaks.
Leaks can be tricky to find. Good luck and let us know what you find out.