Concerning the left intake manifold being hotter than the right - the number 3 cylinder is known to run hotter than any of the other cylinders. That MIGHT be the source of the heat.
Concerning the flow - you say the linkage seems aligned. Can you look down the carb intakes at 3000 RPM and verify both throttle plates are open the same amount? Maybe using a "feeler stick" or something. There is a lot of monkey motion in the actuating linkage, perhaps it only LOOKS aligned?