Have to light the pilot every morning, then furnace fires up but fan short cycles for about 4 minutes then goes off and comes back on.When the fan goes off the burners stay on. Will do this for a while. Then the pilot will go out or the gas valve shuts it off for no reason and I have to relight it. Has been doing this for 4 days now. I have replaced the thermocouple. Any ideas?

Thermostat problem not coming on on temp fall bridge out stat and see if it lights

https://diy.stackexchange.com/questions/130130/furnace-runs-for-about-5-minutes-only-and-shuts-off?rq=1
Why does my furnace run then stop? A common reason a furnace short cycles is because the heat exchanger, the part that heats your air, is getting too hot due to a lack of airflow. Once the heat exchanger overheats, it trips the high limit switch, which shuts the furnace down to protect it.Dec 9, 2016

The fan is activated by a time delay switch on the control board. But before you spend big money on a new board check these things. 1. Is the blower wheel clean. 2. Is the filter clean if you have one. 3. If it has a/c on this unit and has been run without a filter the evap coil may be packed with dirt causing and overheat situation. 4. Do you have any collapsed ducting or room vents shut off. Is it cycling on the limit switch. (you can test this with a thermometer, first measure the air temp entering the furnace, usually at the return. Second measure the air temp leaving the furnace. as close to furnace as possible. The difference of these two numbers is temperature rise. Check the label on the furnace and it will give you the rated temperature rise for that furnace. Take these measurements after the furnace has been running 10 minutes to get an accurate reading. If it exceeds the maximum rated rise the heater has an air restriction or blockage.) You can also jump the two wires going to the limit and run it through a cycle to see if it still short cycles afterward. If the problem goes away then you have an overheating issue. If it continues its probably the board.

The first thing I would do is make sure the flame sensor is clean, this is a metal rod immersed in the burner flame on the opposite side of the igniter. If too much oxidation builds up on it, it will not allow the burner to stay lit. To clean, just turn off furnace and remove flame sensor and clean with steel wool and then reinstall. If this does not solve the problem there may be a problem with the gas valve.

Goes out or is blowen out ? could be a short pilot needs cleaning

Thermocouple could need replacing or the heat exchanger is split and the fan is blowing it out

Wait 30 minutes; press reset button. Repeat if necessary. 4. Pilot light out. 4. Relight pilot. 5. No gas. 5. Make sure gas valve to furnace is fully open. Not enough ... home.howstuffworks.com/how-to-repair-gas-furnaces1.htm

Just checked this site. I am sure you will find it useful - Good luck

Try cleaning your thermocouple,and resetting it where was, which is located at the pilot flame. this should solve your problem.

Good Morning, So, you say the heater does heat up, the fan will cycle on and shuts back down in a minute, and continues to cycle this way. A few things that will cause this. But let me ask this first, does the burners stay on through this short cycling of fan? Let me know if we don't solve it before that. I don't know if you're t-stat is programmable or a mechanical? Anyway, you have what they call a heat anticipator on stats which will cycle unit on and off like this if they have burned out. If it is a mechanical (mercury switch) type, pull the cover and you will see a small dial with numbers and a arrow on it. Set it to .4 and if its programmable, you will have to go into the program to do this. Normally it is set at factory to .4 amps and the setting varies with the amps on the gas valve as they should match. I assume you have been there for sometime and this problem has just started.I wish I knew if the burners were shutting off when the fan cycles off? This would be helpful. If the burners stay on because the fan is only off for a short time, the high Limit switch is good, because when the burners are on, and the fan comes on and shuts off and stays off, the unit will open the contacts on the high limit and shut burners off for safety. I would say that the combination fan control is sticking or failing causing your fan to short cycle. Only, if this is an older furnace though. If it is a newer one with the electronic pilot ignitor, the main control board is you're problem and will need R & Ring. Please get back to me and give me the information I have mentioned, as name, model #, serial #, and age or if it is eletronic pilot or a standing pilot(on all the time) this will help to solve this. Also, what stat you have.Try the things I mentioned, but please get back to me so we can solve you're problem. Thank you, and Sincerely,
Shastalaker7

If the burners do not fully ignite, the sensor will shut the furnace down. The lack of sufficient burner flame is a gas valve or gas pressure problem within the valve.
Replacing the gas valve with the original one may get you going. I surely suggest a professional service company for safety reasons and a thorough inspection. A 20 year old furnace is past it's normal life span.

Make sure all the wire connections are good and tight. Next lift off the cover and look for a little thermal disc mounted up by top of the heat exchanger. Most have a re-set button but not all. If you have this ,by-pass it ,see if that solves the problem, if so it may be defective, or doing its job and you have a venting problem. If you don't have this and have changed the thermocouple (was it a copper tube with a fitting that screwed into the gas valve, or did it have 2 wires, that is a pilot generator, kind of same thing) make sure the probe is set correct, with the pilot flame heating the top 1/3rd of the probe. The only thing left is the gas valve.