1) Yeh... as you already mentioned, you clipped the pedal at the bottom of the frame. I would have shot at a higher angle to give the flower more 3 dimensions. The white and the ruffles in the pedals make it difficult to distinguish far and near.
2) Settings don't matter... but the final print does. DOF is good. You can soften up the harsh shadows a little with a fill flash. I think the settings you used are fine.
3) A little fill. A slightly higher angle. Closer up if you can.. fill the frame
4) In PP, I would probably clone out the one lone green leaf at the bottom left.