Funny you should post this. I am re-gearing my Dana 30 right now, and contemplating what I am going to do for seals.
You are correct, that most aftermarket seals will not fit over the disconnect shaft as it is larger. I don't remember the actual size- but its about a 1/4 larger diameter than the drivers side shaft. The disconnect splines are the largest part, and may prove difficult to get a seal over it, yet still seal to the shaft at the outboard end.
I have nearly come to the conclusion that I will build my own seals. You can search for a seal with adequate specs pretty easy on the internet. Ive found a few for ~$6, available at Autozone locally. What I was thinking, is casting a whole assembly, seal "housing" and seal in one piece of polyurethane, or as a plan "B", casting a seal holder from polyurethane and buying a replaceable seal to insert into it. I think if I chose the right hardness polyurethane for a one piece seal/holder, it would seal nice enough to the inside diameter of the housing, and provide a lip seal durable and pliable enough to ride the axle shaft. My friend does composites and mold making for Disney. I plan to get his opinions very soon, so I can decide if I want to try this or not.