Toyota Repair: Air Intake Missing Part, vac line, master cyl

Question
Hi Ted! I have a 1995 Camry LE 4 cyl with 149K miles. I was having derivability issues, but have worked out a few of them. I did notice something missing from the side of the intake manifold on the timing belt side of the engine.

The air intake has five holes drilled in it on the timing belt side of the intake. One hole closet to the passenger compartment on the intake has a small vac line connected to a metal line that is connected to an electrical connector that is attached to the number 1 air intake tube on the manifold.  The hole in the very top center of the air intake has a short about half inch thin metal tube in it with a piece of PVC or very hard rubber on the end. Looking at this makes me think it is like a "plug" for a hole in the intake. There is also another one of these plugs on the back of the intake facing the passenger compartment.

On the top front of the manifold is the vac line for the brake's master cylinder. Below this master cyl brake's vac line connection on the intake manifold is a hold drilled into the intake that has very clean dirt free looking threads in the hole. I was wondering what this hole is for, Ted? Should this hole have a threaded plug with a rubber like cap on it like the other hole on the top of the air intake?

Below this threaded hole is another vac line running from the bottom of the air intake to a point that looks like it is under where the air intake connects to the block.

All the other exposed threaded holes on the air intake have rather dirty looking threads. Since the threads are clean on the threaded hole below the brake's vacuum fitting, I am wondering if something shook out of the motor like a rubber capped plug or something else?

Thanks Ted for your input!

Answer
Any openings in the intake manifold will have an affect on driveability, the first two you mentioned that have the rubber caps seem normal, the threaded hole with nothing connected is not, it may be that's where the connection for the PCV valve should be, I really don't know, I have no history of what was done to the car so more information may be needed as to when did this problem start and was anything done to the engine recently that could have caused this.