I changed intake gaskets on 02 chevy malibu 3.1L car starts then stalls or runs rough.I had it runing for 5 min. it idled 2000 rpm and up. Why?

run fault codes to find the faulty sensors

The website has software that looks for obscene words.
I would think a compression test would show if the cylinder is having mechanical problems. And yes the intake or head gasket could be leaking again, especially if the intake or head were warped or cracked.
Have you checked fuel pressure ?
Does the spark plug for cylinder 5 show signs of coolant leaking into the cylinder ?

Engine stalling and rough run issue at low speeds

This problem is commonly caused by a dirty automatic idle speed control valve and throttle valve. Buy a can of throttle valve cleaner (do not use carburetor spray cleaner!) from NAPA or Carquest (made by CRC chemicals) and spray it into the air intake while the engine is running, use up about 1/2 the can, engine will try to stall hold the speed up, shut it down and let it soak for 30 minutes, restart and blow out the remaining fluid, shut it down and disconnect the negative battery cable for 5 Min's to reset the base idle control

Engine stalling and rough run issue at low speeds

This problem is commonly caused by a dirty automatic idle speed control valve and throttle valve. Buy a can of throttle valve cleaner (do not use carburetor spray cleaner!) from NAPA or Carquest (made by CRC chemicals) and spray it into the air intake while the engine is running, use up about 1/2 the can, engine will try to stall hold the speed up, shut it down and let it soak for 30 minutes, restart and blow out the remaining fluid, shut it down and disconnect the negative battery cable for 5 Min's to reset the base idle control

Here are the most common causes of idle surge, rough idle esp when cold, other symptoms include stalls at stops, slow idle speed, erratic idle speed, rough idle and engine hesitation (and other problems), it is in most cases the idle speed control air-bypass valve and or throttle valve and upper intake, these area's get full of gunk and combustion residue over the miles and cause idle issues (stalls, low idle) like yours, Get a can of intake cleaner from any local parts store, not carb spray, intake cleaner, it is made by a company called CRC, remove the air intake hose to the engine, hold the idle high so the engine won't stall, then spray the can of cleaner into the intake while keeping the engine running, use at least 1/2 the can, shut down the engine and disconnect the battery for 5 minutes, then restart and complete a number of mixed driving cycles, town, freeway, stop and go etc., after a few days the problem will go away as the system will relearn to the clean intake

For this types of problem,there are few help inks to troubleshoot the problem.Click the link below to go through the troubleshooting procedure to resolve the issues :----Idles rough and quits when gas pedal is pressed less? http://technoanswers.blogspot.in/2012/01/1999-ford-f-150-idles-rough-and-quits.html-----------van idles rough? http://howtobyme.blogspot.in/2012/01/2004-ford-freestar-van-idles-rough.html
--------------runs lean and idles rough? http://technoanswers.blogspot.in/2012/02/ford-runs-lean-and-idles-rough.html
-----------Car still runs Rough after tune up? http://howtobyme.blogspot.com/2011/12/car-still-runs-rough-after-tune-up.html
------------Idle flair is noticed on car? Rough idle? car will not idle? Erratic idle speed? http://technoanswers.blogspot.in/2012/02/idle-flair-is-noticed-on-car-rough-idle.html
----------High rpm in neutral? Inconsistant high RPM in neutral? http://technoanswers.blogspot.in/2012/02/high-rpm-in-neutral-inconsistant-high.html
------------Engine Backfires? http://technoanswers.blogspot.in/2012/02/jeep-backfires.html----------- Nissan stalls and bucks on Acceleration?

http://technoanswers.blogspot.in/2012/02/nissan-pathfinder-stalls-and-bucks-on.html

-----------
Nissan Pathfinder Backfires? http://technoanswers.blogspot.in/2012/02/nissan-pathfinder-backfires.html
---------How to adjust rpm? http://schematicsdiagram.blogspot.com/2011/12/how-to-adjust-rpm-on-2009-dodge-charger.html
------------Engine cuts out at 3000 RPM? http://schematicsdiagram.blogspot.com/2011/12/engine-cuts-out-at-3000-rpm.html
----------This will help.Thanks.

It's been almost 2 years since you posted the question so it's likely you will not see my answer to your question.

First, do NOT make any adjustments to your throttle body idle setting. The screw most likely never budged since 2006 so you should not touch it since this is not the root cause. But yes it is wise to check all vacuum lines as "craig" suggested.

I have a 2007 Corolla CE, 1.8 liter VVT engine, 5 speed manual transmission which I bought new from the dealer. Currently has about 108k miles on it. After about 4 or 5 years in cool to cold weather it started doing the same thing. I researched it online then asked my local Advance Auto Parts person who confirmed my hunch. It is known as "idle hunting" when the engine is cold, in colder outside temperatures the idle rpm's will increase up to roughly 2000 rpm then drop to idle, then back to 2000 rpm, then repeats multiple times. Then after driving a short distance, stopping and running at idle, the idle speed may drop to 600 or 500 or as low as 400 rpm, running quite roughly but still keeps running. My Corolla normally idles smoothly and steadily at 800 rpm when warm or hot. The idle hunting or low idle rpm will typically correct itself when the engine warms up enough.

The problem: the intake manifold gasket has aged and shrunk a bit, allowing engine compartment air to get pulled directly past the gasket and into the cylinder head intake port. This causes an imbalance between the reduced air filter airflow sensed by the Mass AirFlow (MAF) sensor versus the actual air/fuel ratio versus the engine rpm versus the oxygen level in the exhaust stream. The gasket will shrink more as the temperature under the hood drops, allowing more air to flow past the gasket. The Engine Control Unit (ECU) is simply trying to do its job as programmed by increasing fuel delivery to compensate for the overall imbalance, then when rpm's get too high it will reduce fuel delivery.

The solution: purchase a new intake manifold gasket for roughly $10 to replace the stock gasket. Mine is a thin orange polymer gasket with round cross-section which seals around all 4 intake ports. You can search for instructional video of how to install it on YouTube.

I purchased one but did not install it yet. I am sure this will resolve the problem since all other suggested fixes I found on the internet did nothing but unnecessarily frustrate the owners.

idle learn procedure:

turn off all electrical items (AC fan, audio, lights, defogger, etc.)
Start the engine and hold it at 3,000 rpm with no load (in park or Neutral) until the radiator fan comes on or the engine coolant gauge shows normal running temp.

Now let the engine idle for a minimum of 5 mins with no electrical loads. If the radiator fan cycles on during this time, you must add the fan running time to the 5 mins.

Vacume leak or bad idle motor. With the car in park and running with the hood open listen for leaks moving your hand around the different hoses looking for a change in the sounds that you hear. The idel motor also makes the car idel up to 1500 RPM or so right at start-up then idel down, If it doesn;t the idel motor is likly. Check engine light is on when running? Test for codes, Follow code test charts don't skip any steps!.

HI!!! first try this get brake cleaner.go little bylittle spraing all around the intake if run normal and changes the rpm.you have intake leak' o change idle sped sensor