Throttle position sensor. Root of all evil things EFI.

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If you have an O2 sensor before and after the cat, not running a cat can play hell with the ecu, since the readings after the cat will be the same as before, the ecu will lean the engine to try and compensate for the readings.

Just buy a new cat from Autozone for about $55, or if you want to spend the money get a Magnaflow Hi-flow cat. There is some difference between the two, the Magnaflow is easier to see through. There is no benefit gained from running a 22r w/o a cat, you actually lose buy polluting your air more.

mine ran much better without the cat and stock muffler.maybe it had problems anyway

A clogged cat will inhibit performance, as well as a bad or stock muffler. The oem muffler is designed to be quiet, not for performance. A budy of mine with a carb'd '84 punched a whole in his cat(could easilly afford to have a shop put on another one but he is cheap) when it was clogged, which did help some, he also ran a header and highflow muffler. Since we live in state with mandatory smog inspections every 2 yrs, when he put a new cat on, his performance actually improved, that little bit of added back pressure really helped. Standard 22r's don't benefit from a completely open exhaust system, unless you are always running above 4k, which is hard to do unless you are racing, they simply don't produce enough power.

The other thing to consider in the big picture with intake and exhaust is you will only get coming out essentially what went in. For instance if you have a restricted intake (plugged filter) you can open your exhaust all you want but nothing will improve. The other way is run perhaps a K&N to allow more air in but if your exhaust is plugged your not going to gain. Don't get me wrong there are other factors involved such as air volume, air/fuel ratio, back pressure etc.

How can one determine if their cat is clogged?

Does it need to be removed and visually inspected to see if any light passes through or is there an on vehicle test.

My 87 has 163k on it and I'm wondering if a new cat might wake it up some. I put on a 2 1/4" cat back with magnaflow on when the stock exhaust rotted and fell off and this has been a HUGE difference but the 4runner is heavy enough and since I'm at altitude I need all the power I can get.

Compressed,
If you've got some way of measuring the temperature going in and comming out of the cat converter, it will help tell. Hotter out means it could still be working: Same temp in and out means it's bored out. Saw an infared temperature sensor gun on sale from a company called Harbor Freight that tempted me the other day. That company's great for selling seldom-used odd tools, but we don't help the American economy doing so, I'm afraid to say.

I don't know about your e-laws in your state but I pull the cat off and take a look down the hole to see if its plugged. If it is leave it off and run a straight muffler out the side. You will see a big difference. And the noise isn't that bad.

the tempature should be about 100 degrees F hotter after the cat.

The cheapest way to tell is just pull it off and look through it. If you can see light on the other side(about the size of a dime) than it is still good. If you fcan't, or it is rattling replace it with a new one. There is a bit of difference between the standard hi-flow cats and the the Magnaflow. There is a lot more light visible through a Magnaflow, and you can almost make out what you see, whereas you can't with a regular cat. However teh Magnaflows do cost a lot more.