Sorry, I must of missed this for some reason.
The reason your plate is bent is because the factory applies a shittonne of silastic to prevent the rather inadequate seal created by the CARC being bolted up to the swingarm allowing oil to leak into the swingarm and drop out of the hose clips underneath that carry the brake line and speedo cable. It's so thick and sticky that as you prise the box off the plate will warp.
Don't worry about it. The row horrid little self tapping screws that hold the compressing plate on aren't there to seal anything, just to line it up. The actual sealing is supposed to be done by tightening up the bolts that hold the box to the swingarm. Problem of course is it doesn't work brilliantly. Hence the snot on later, (Post2010-ish.) bikes.