The pistons have be removed from the top of the block while the crankshaft comes out from the bottom. The cylinders are tapered, wider at the top and smaller at the bottom, not allowing the piston to exit from the bottom.
You have to remove the rod bearing caps and push the piston and rod assembly out the top of the cylinder. If the rod caps are attached with nuts to studs, you need to ensure the threaded stud doesn't scrape against the rod journal and damage it's surface. Tape around the stud threads or maybe short pieces of soda straw slipped over them will protect your crank.
Once the pistons are out, you can remove the main bearing caps and lift out the crank. Although, it sounds like you've already taken the main caps off. If so, I encourage you to put them back on finger tight to help support and stabilize the crank while you're removing the pistons.
Good luck.