The trick to getting the valve covers off of an E-body with a hemi is recentering the engine slightly when using a motor plate. Mine is centered as close as possible, and then with the Indy valve covers, the end bolts aren't needed because they use a small stud in place of them. Mine clear everything. The other thing you can do is run the master cylinder off the adapter plate Mancini sells and that mounts the master with two studs as well. Plumb it up with AN03 or 04 braided lines, and you can move it out of the way when needed. Mine is done that way, but it all ended up clearing.

Take a look at my link to the photos and vids in my sig below.