Answer in progress (see comment to the question for clarification questions).
Checking spark plugs and spark
First thing I would check is condition of the spark plugs and quality of the spark on each cylinder both before and after warm-up.
- Take all the ignition wires off the plugs.
- Pull the plugs out, and check their condition: look for soot contamination, any difference in glazing, damage to the ceramic insulator and/or evidence of flooding (it would be wet with petrol). Use this reference.
One by one, check each plug (make sure other plugs are out to avoid starting the motor needlessly) by putting ignition wire on, touching the ground electrode to the engine casing, and cranking it to see the spark. The spark should be nice, big and blue. If it is too weak, or different colour, we might have a culprit.
Safety Note: checking the spark that way is easy, but be careful not to get shocked (especially, if it could be spark plug wire boot shorting). Shock can be noticeable, but not too dangerous (unless you have heart pacemaker or somesuch) as voltage is high, but amperage is low. If hesitant, best use the special spark testing light (though it shall not rule out any particular bad plug).
- If one of the plugs has no or poor spark, check this plug on known good wire, and, conversely, check known good plug on that wire to determine whether it is a plug issue, or supply (then we shall be checking wires, distributor and so forth).
- After thoroughly checking everything out, put everything back on as it were, then warm up the engine (best by actually going somewhere on a short errand if at all drivable), and repeat the steps to see what has changed once it reaches proper operating temperature and starts to work fine.
Make sure to be thorough and cover all the steps so as not to miss any possibility. Check back after it is done.
