For road racing I think I'd be tempted to run the 3.79 stroke crank with a longer 6.25" rod to keep the side loading down and with a solid cam you'll probably make very close to the same top end power with the same compression and cam. You should wind up with close the same CH and weight piston as a 4" stroke with a 6.125 rod but your rod ratio and piston speed will be more favorable for SUSTAINED High RPM use.

You can have too much torque coming off a corner and the compression braking might be a bit less herky jerky with less cubes. I know this from my experience with Cobra replicas that most guys prefer the 3.85 stoke 393" motors with longer rods that keep the side loading down and a wider more tractible powerband with less likelyhood of an overrev....not so much an issue with drag racing but the way oil moves around in a road race car is quite a bit different.

Also I'd run the 340 block with it's smaller mains, Canton makes some pretty good road race pans.

so a 395" (4.07 x 3.79) would be the way I'd look at going with a Tremec 5 speed, I think you'd make as much power as a 416 with more of a rev cushion up high.