The front cover can come off, maybe have your machinest measure it while its on the block, take it off and shave it down. I don't think its critical to have it perfect as long as it isn't high. But as close to perfect as possible.
My chevelle isn't numbers matching or a SS but I'm building a Pro touring car with most likely a supercharged or turboed LS1. I have a painted chassis with all hotchkis suspension, tall spindles in front with 13" baer brakes up front with a moser 3.42 posi in the rear with 12" baers. It's going to be sweet! But thats on the back burner for the supra build