On a low deck the 4.25" 6.535" 2.200/.990 (BBC journal & Pin) Rod bottom end is proven strong and reliable and not too hard on the block side loading, it gives you about a 1.32" Compression height piston. If I were going High dollar block I think I would opt for a 6.700 rod, 6.800" is doable as well but it puts the pin way up in the piston/ring pack.

but If I were going aluminum block I think I'd just go all-out and get an RB and maybe even a raised cam core and go BIGGER on the stroke and long as possible on the rod. Why build a 540 when you can build a 605 for the same $$$. the weight savings is in the Aluminum block, 605 is like an extra cylinder's worth of displacement.