OK so my 2001 altima has been shaking when stopped at a light and idling. Also has started shutting off.

Went through and replaced spark plugs, wires, distributor cap, rotor, valve cover gasket, and oil.
Also checked the hoses for an air leak and came up with nothing.

HOWEVER:
I just started messing with things to see if anything would change. And I found that when I pulled the intake hose off of the throttle.body completely and then started the car it ran perfectly!

I tried to put it back on and it ran rough again. I also tried taking each hose off of the main intake hose after it was placed back on and that made it stall out...

Please help I can't stand my car sounding like death anymore!

sounds like the mass air flow is failing. what you did by pulling the intake off and starting it is usually one of the methods to troubleshoot a bad mass air flow. my 00 sentra was basically doing the same thing. i replaced mine and everything was back to normal. you should though check to see if the sensor is covered in any type of debris or is just really dirty. if so, clean it off with some mass air flow cleaner that you can get at autozone or just about any automotive retail shop and see if that makes it run better. if not then you may need to replace the mass air flow. hope this helps!