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I wounder if you got the wrong flex plate to begin with ?
And like what was said. if the starter gear was not retracting all the way back in. it would drag on the flex plate a little at a time and eventually machine the teeth off.
If your crank was that far out, or out in any manner. you would loose MASSAVE oil out of the rear seal. There is no way it would not leak oil...
you could of had gotten a bad flex plate to begin with. It happens, it could have been slightly bent also..
Avoid Ford - they will likely soak you $2K by the time you're out of there. I would either find a Ford diesel-savvy mechanic, or DIY and post photos here. This forum will have all the expertise you need.