Since your starting from scratch the bigger motor probably won't be any more expensive so I'd go for it. I just wouldn't push it to the point where your having to run a shorter rod on a long stroke.
I can go with a
6.125" rod with a 4.0" stroke 428 cubic inches = 1.200" from pin CL to top of piston.
or
6.0" rod with a 4.0" stroke 428 cubic inches = 1.325 from pin CL to top of piston.
or
6.0" rod with a 4.125" stroke 441 cubic inches = 1.2625" from pin CL to top of piston.
In a perfect world I'd want 441 cubic inches and it would give me a little more on the top of the piston.....
What you think? 6.0" rod too short?