Loverid, welcome to the forum and congratulations on your new boat! The pedals rarely come perfectly aligned from the factory. It's an easy process to fine tune them though, especially with the '08 or newer Drives. While you're at it, check your cable tension and make any adjustments as you align the fins.
With some of the hull shapes (like the Revolution and Adventure) it is possible to smack the hull bottoms with the fins. When you get your boat in the water, you should set the pedal positions so that the pedals do not normally thump against the hull with your legs extended (without hyper-extending); a slight fin misalignment would not normally be noticed operationally. If someone is experiencing noise from the Drive, it is most likely due to the pedals being adjusted too close.
There is a variable amount of slop in the crank arms where the pedal adjustment pin goes through. Again, when you're pedaling, this should not end up as an issue as your leg will keep the pin pressed against one side as you pedal. If it is bothering you, show it to your dealer and ask his opinion.