for the throttle - check if it catches in the insulator, and definitely have 2 gaskets in. if that's not it, the only thing i can think of is that somehow when you torque it down it gets bent or there is something getting in the way (screw, nut, gasket, hose) - also take a flashlight and look down with the butterfly open and see if the intake and the spacer is centered with the carb.
for the puffing on the pcv valve - take a compression test (i just did that) - one of my cylinders is lower so i guess that's why i get some blow-by, make sure both of those fittings (the ones that go on the intake) are really clean and free of any obstructions, i would take them out and clean them really well, when you have the throttle closed you should see air going into the breather in the rear of the engine and not the other way around. A compression test will confirm if it's a bad cylinder or not.