I'll take a shot.
Strokers increase the size of the combustion chamber by increasing the piston vertical travel. Yay more CCs!
Torque is increased since the distance from the center of the crankshaft is longer. (Think a lever and a fulcrum, further the end of the lever is from the fulcrum, the more leverage you have)
Rods are lengthened to limit the angle the rod most extend to reach the far extremes of the crankshaft. Short rods have to rock back and forth on the wrist pin further (Larger angle) than a longer rod.
Cases have to be moded to clear a stroker crank. All of the spacing has to be correct. Modifying domes, adding spacer plates to meet clearances. May have to




around a bit more depending on how your ports will line up after all is said and done. Wear on your pistons and sleeves are increased. Sideways forces are greater on the connecting rods if they aren't lengthened appropriately. I'm sure I'm missing some




.
Yamaha probably determined their engine specs by figuring out what is cheapest for what they are looking for in reliability and power. Besides, even if their cranks came stock 78mm instead of 68mm, we'd all want more still.