I think I'd probably run that. Those pistons were most likely made for a 3.98 stroke, being that they are domed pistons to start with. If they were flattops, I might worry more about deck thickness. From your pics, the VR are not very deep, and .140 down is pretty darn safe. I used to run .125 down and huge VR in Super Stock 428's. The exhaust relief was thin in the corner, but we never had any issues. The key part of your question was the part about being naturally aspirated. Any kind of power adder throws everything I just said up there out a 40 story window!!