Tom,
You are correct that the engine has to come out of the car to get the oil pan off. The windage tray interferes so there is not enough clearance between the engine and the frame, even if you jack up the motor. Most likely the two little rubber seals that go between the rear main cap and the block were not installed. I made this mistake many years ago when I built my first 409. Be careful, when I did this repair years ago, I took the engine out and one thing led to another and before I knew it, I was was doing a frame off restoration.
I attached a picture of the two little rubber pieces.
Good luck,
Frank