Fortress 49
I will try to answer as best I can with your questions. Remember these are just my thoughts and opinions. In other words, it doen't make them right. :-D
Advantages of 32" over 28"? This is based on personal preference only. In my experience when you get this long of barrels they have no difference in performance. Go with what feels best for you. I prefer 28 or 30 inch.
Advantages of 3.5 over 3 inch guns. The only advantage in my opinion is more shot, which leads to a higher concentration of shot at the target. From what I have read, the velocity is usually the same on the two shells. Disadvantages for these loads is the 3.5 incher's kick more. If you go with an auto, no problem. The NEF's will leave a reminder on your shoulder. :-D
Distance difference in Mod and Full? Don't know the answer to this one, but I would not shoot any waterfowl loads through a full. The hard shot patterns tight anyway and the full is to constrictive. It also can cause barrel damage on fulls if you shoot steel through them a lot.
What chokes and barrels for your NEF? If you are going to use it for waterfowl, go with the Deluxe Classic Barrel in 12 gauge. It has a vented rib barrel which really helps me in shooting (I love mine). If you don't want to spend the extra for the deluxe, I would get the longest 12 gauge available in Modified choke. This will also work for doves as you requested.
24" or 32" for high flying geese? No question here, go with the 32". For me, the short barrels are hard to follow through with on the long shots. I never feel comfortable with the short barrels while hunting waterfowl.
If you are going to shoot high flying geese, spend the cash and buy some Hevi Shot. You won't be sorry.
Good luck with your NEF. I take mine duck hunting from time to time and really enjoy the single shot challenge.
Hope this helps.