Need help with rough idling, 4 Runner

I have a 1994 Toyota 4 Runner V6 with 125,000 on it. It just recently started idling really rough like it is barely running. It has no power. We have changed the plugs, made sure it is getting spark, have changed the distributer cap and rotor as they were trashed. Nothing helped. There are several things going on, first the part that holds the air filter, when you take the air filter (has a K & N) out and listen their is a lot of noise coming from that part, 2nd when you pull off one of the plug wires, while it is running and have it running on 5 cylinders instead of 6, the idle never changes like it does not phase it one way or another. We bought this used from a little dealership just about a year ago. I am thinking vacume leak, distributer itself, timing belt is worn or stretched possibly, never got enough stuff torn apart to find it so am not sure on that. I have an idea that it is on the front of the motor but their is some junk in the way. Could it be a fuel problem? Why is it idling so rough? Where did my power go? Why does the idle not change one way or the other when running on 5 spark plugs or 6? Why does the Air Filter housing (or whatever that big contraption that holds the air filter is called) make noise? Where do I start and what are we looking at as far as repair costs?