One thing that will help is using bolts to hold the valve cover on instead of studs. Studs do make everything else easier though. You will have a little more movement w/o studs to help clear the fender.
Yes, I should have mentioned that also. My entire engine is mostly studded including the driver side rocker cover. Except for the passenger rocker cover for this very reason. I have 12 point s.s. ARP bolts in that cover.