in that first pic of the heat riser,you don't have to worry about blocking the hole on the exhaust manifold because it isn't a hole it's just a port that leads directly to the manifold.Stick your finger in there while the engine is cool and you'll see what I'm talking about.
In your second pic of the "flapper",LOL,What I did for my homemade snorkle(assuming you are going to retain the factory airbox) was cut the square part off flush with the airbox and then I took the "flapper" and siliconed it over the square hole in the air box....fit perfect and is water tight.
Let me know if you need pics....
In the third pic the arrow on the left points to the "octopus" as alot of people call it.I completely deleted this mess of vacuum leaks a while ago....it really isn't needed if you get rid of the EGR at the same time.The hose that you are holding in your hand is part of the evaporative system that vents fuel vapors from the charcoal cannistor to the intake,you wanna keep that unless you delete the entire evap system(not recommended)
The arrow on the right I believe is the vac line that controls the "flapper" if so plug it off or it could be the vac hose for the EGR transducer.....