Joshua,
Not sure what you're trying to do if you've decided to replace the power train, but before you do much with the flathead I would drain the pan and see what comes out (if you didn't already do that). If it is full of water you need to consider pulling the pan and seeing what you've got, but at the very least you need new oil in the crankcase, and I would also squirt a couple of shots of motor oil in each cylinder for some lubrication on the rings if you're going to be cranking it to see if it fires. Like Rrumbler says, do a bit of trouble shooting on the starter, or consider pulling it and taking it to your local parts house for a condition check on their test rig. Are you just checking out the flathead, or trying to get it running?