1. The 400 block has "siamese" cylinder walls - no water can flow between them. Just use a good water pump and a good radiator and you'll be okay.
2. Because of #1 air can get trapped just under the deck of the block in th ecrotch of the cylinders... so 400 heads have "steam holes" drilled in them so the air can escape into the water passages in the heads - some water will flow there also, but the holes are small - 3/16". You may use those 350 heads, but drill steam holes in them. It's not rocket science... but you do need to drill them in the right place(the 400 head gasket will show you where) and at the right angle. Car Craft should have the article online or a Google search will should find it. You can do it because you're a hotrodder.
3. You're right about the longer rod reducing lateral pressure... and that's a good thing, BUT you do need to use pistons designed for those longer rods. Pistons for 6" rods are lighter(a good thing) and the piston pin is located closer to the top of the piston - it is usually up into the oil ring... which is okay because they make a special ring that'll keep everything in perspective.
4. You're not bending that 6" rod over your knee. It's either being compressed or pulled apart. The rods(and rod bolts) do take all the punishment in an engine... that's where you should spend some money. Today's rods and rod bolts are of excellent quality. Don't worry about breaking them unless you're taking the engine "upstairs" - 7000-8000 rpm
Buy a rotating assembly that's balanced. A cast crank is fine for up to 6000 rpm. A 400 makes an excellent low rpm high torque monster... 170-180 cc intake runners and a 212-218
[email protected] cam, rpm intake, a 750 4 barrel of your choice and you won't believe the power. It's awesome.
Good luck with the project.
Bob