Longer stroke is going to side load the pistons more. This will create additional friction, more windage in the crankcase, etc. For your uses, I think I would go with a 4" stroke and some ported Indy oval port heads. When I worked at a machine shop last, I built a 408 using a stock magnum block, ARP main studs, a hydraulic roller cam of specs I cannot recall. Ported Indy oval ports that flowed 327 cfm at .650". That little engine made 590 hp. If it had a solid lifter cam in it it would have exceeded 600 easily. The hydraulics wouldn't support the rpm though. And the magnum blocks need a tall lifter to clear the block. Regardless of what you choose, I think you'll be happy with either. I just think the shorter stroke will last you longer.