I've had the available options vary depending on the connection time, which at least for domestic travel needs to be 4 hours or less, and which often changes with minor schedule changes when the connection time was already close to 4 hours. Look at each portion of your hypothetical itinerary (either as nested roundtrips or as one-way booking for each segment) and see what combinations meet the 4 hour rule. With just the right amount of bad luck, there may not be any "legal" connections for the route you are planning within the allowed time window. (I don't know if Delta has different rules for connections to international flights.)

I've had flights for a particular time of day disappear and then later reappear when a later schedule change puts the connection time back under 4 hours. You could always book two roundtrips (nesting the Japan flight within your trip from Fort Wayne) but that will likely be more expensive. Delta did link the trips the one or two times I've had to do that. Or travel out of alternate airport.