Ok, the most likely point where the water would get in, in that situation would be the seals on the driveshafts bearing carrier (located beneath the waterpump) - assuming that the (new) gearcase is not cracked somewhere between the water pick-up and and the waterpump base.
But before we even go there, sorry, just want to back up a little again and ensure you checked out this lower unit before you bolted it on.
It had gear oil in it and looked fine first - then you tried to run the motor and after that the water came out (or) you just bolted it on and tried (so the water may have been there when you got it)...