Oil starvation can do a lot of damage, so inspect everything carefully before doing a buildup. How bad was the failure- - - -did the engine lock itself up, or just hammer the rod bearings and crankshaft? If you're going to hotrod it, definitely get a line-bore done before fitting a new crankshaft. Pull all the oil gallery plugs, and scrub all the passages with a shotgun brush and solvent, followed by a thorough pressure wash.
The "steam" holes are for coolant circulation between the siamesed cylinders. As long as you use the original 400 heads, no problem- - - -they're drilled to match the block holes. If you decide to use 350 heads for more compression, use the 400 head gasket as a template to drill the steam holes in the heads between the cylinders.
400's have a bigger bore (4 1/8") and a longer stroke (3 3/4") than a 350. Their main advantage is torque, due to the longer stroke. The long stroke makes it difficult, if not impossible to put enough counterweight inside the crankcase to balance the crankshaft, so an off-balance harmonic balancer and flywheel is used. 400's DO NOT like high RPM! Put a relatively short-duration, high lift cam in it, and try to keep the RPM under 6,000, and you'll have a torque monster! A set of 76CC cylinder heads with enlarged exhaust valves (1.6") and some pocket porting will give you good compression and good enough breathing to support good low end and midrange torque. Just don't expect to be able to run the RPM that you can with a well-built 350.
Jerry