Have you tried to run the boat onland hooked up to a garden hose at the strainer??? Make sure the connection is water tight and look for water entering the bilge area. This test will eliminate the water entering from the engine side and then you can look more in detail for underside leaks.

Ever thought about the skegs on the bottom side of the hull?? You said something about beaching the boat, and got me wondering if the seal there could be the culprit. A tube of 5200 will go a long way......