Hi Asher,
The 2x extender is the standard Canon extender (teleconverter). I don't think I've ever focused manually with the 180mm macro lens, but when using it plus extender and 25mm extension tube with the 5D, I'm sure AF would not function.
I used a tripod while sort of sloshing through shallow water and mud. I don't have a macro rail, but probably will if I finally get around to picking up an MP-E65mm macro. The combination of stuff with the 180mm is a stop-gap until I make up my mind about this macro lens. I'm not totally convinced the extreme magnification of the MP-E65 is worth the extra weight and loss of flexibility while hiking in the woods.
As for composition, I picked the vertical because the frog was hiding, and I knew if it became any more startled than it was, it would have leaped into the water. The open water in the foreground was its escape route, and it seemed an important element at the time. The water itself was fairly muddy, so I don't know if increased dof would have revealed any detail worth the effort.
Interesting question about focus bracketting. There's a software application that does this, but haven't had time to explore.
Tom