You're having the normal problems with the cover. If you removed the lines to get a straight shot straight up, you wouldn't need to do any bending. But it's just a flex cover and will not hurt if there are a few tweaks along the way.
What I usually do, is to set the plate in place, and then take the bends out with a pair of needle nose pliers. I then slide the cover statically in place and see if the cover fits well enough? If I need to make more adjustments, I can tell where the areas need to be reshaped. Now I start the car and make sure I don't hear the cover grinding on the flywheel. If it needs more work, I take a screwdriver and begin to bend the problem area away from the contact point. It's straight forward job, and you will see it won't take much to move it back into position.
