The 409 blocks with the X on the front were real late 62 through 65 blocks.They had somewhat better cylinder wall thicknesses and more mass around the main webs around the main cap bolts. They definitely are the first thing I'd look for. The 340 horse 409 in 63-65 had those blocks. Definitely use an X block. No point putting in killer main caps in a block with weak webbing. I would get a steel stroker crank, standard 409 main bearing diameters, if you go with a 3.76 stroke crank, use a 6.135" big block Chevy steel rod and a big block pin.It's shorter and lighter than a 409 pin.Don't use a GM rod.Get a Manley rod or a high strength aftermarket steel rod. Definitely bush the small end, and with whatever piston you need, you want to float the pin. Very good BBC lighter than stock pins aid in balancing this thing, Get whatever light piston you choose, for a front balancer, get the BBC unit that's steel, not cast, and try to arrive at a motor that will balance in the pan, not relying on external weights in the balancer or flywheel. Definitely have a race engine builder fill the water jackets with a good block filler up to the bottom of the freeze plug bores. That keeps the cylinder walls rounder, the main bearing bore centers straighter, and it still leaves capacity for adequate coolant flow. Boring the engine 060" with the 3.76 stroke gives you a 452 inch motor, a 4" stroke 454 type of thing would be 482. You could go into the house moving business with one of those. A steel roller cam is practically a must these days, and with the Z-11 heads, it would move enough air to probably make 650 horsepower right off. Putting it in a 3250 pound car with the right drive train and suspension would get it into the 9's. Keep the piston and pin weight as low as you cn get it without compromising reliability and that leaves more power to move the car instead of using it to combat inertia.
Sounds like a fun project. If you somehow found an original Z-11 block, I wouldn't use it. The correct QM suffix on the block makes it invaluable to a serious collector.
Have fun with your project!!