Sometimes the cover is cracked and then you have to replace it. But a warped cover? news to me, i don't see how you could go wrong if you take your time, and are careful with the assembly.
The bolts are steel i don't replace them unless some Gorilla has been there before.
The rubber gasket is thick and will have preload when assembled, just nip the bolts up against the steel spacer and all will be fine
Make sure the head face is clean and dry, do not use any sealer