Welcome! As a Cummins guy, I probably should take a shot at the new Ford guy, but I'll be nice.
If you've got a detailed aero question Phil Knox, a.k.a aerohead, is the guy to ask. I'm not an aero expert, but I'b be inclined to get rid of the tall cap if you don't need it. A lower cap would definitely be better than the tall one. Lower vs. tonneau is debatable, depending on the dimensions of the boat (consider putting some pics up for us). My first inclination would be to go for the tonneau, or an aerocap (in the ideal world).
My opinion is that a belly pan is preferrable to an air dam, however, it's much more work. I have yet to do mine.
Overall, driving modifications are almost always where the biggest gains are. That being said, you won't have as many options with an automatic tranny.