Two pretty different set ups, both should do what you want. If going to the LS3 You'll need a lot more small items, a way to mount your cable bracket, fuel rail spacers or something because the injectors are different lenghts (there are more then a few ways for this to work), seems to me the valve covers are slightly different but may work, engines like a different camshaft design dependent on heads, the offset rockers and rocker stands, and I feel like I'm forgetting something.
Honestly you could go either way and get to 600 rwhp with boost pretty easy, maybe easier with the LS3 heads.