440 in an A Body?

A little Ultra Blue RTV on both sides of the valve cover gaskets will seal them up with no leaks. (ultra blue is formulated to expand when it comes into contact with oil. I've never had a leak with it)
Maybe you'll have to shim the engine up a bit for better clearance? I have a 440 about ready to get dropped in at the end of the month so i'm about to start having these same issues too. You'd think that by now someone would have made a pan to easily allow us to drop in BB.....