Rough cold running is often caused by low compression. Many mechanics do not check compression properly. Each cylinder pressure must be written down; so they can all be compared after all the cylinder pressures are known. There are two different standards which must be met in a compression test. One is that there cannot be more than 15% difference between the lowest and highest cylinder pressure. The other is that no cylinder pressure can be lower than the factory minimum allowable limit. But a mechanic cannot know the factory minimum compression limit for a given motor unless they look it up in the service manual; and that is something that many mechanics do not bother to do. The minimum compression limit varies considerably between different brands of motors. If the compression is out of specs; no other adjustment or part replacement will make it run right.
Another thing that can cause this problem is a clogged fuel filter. But fuel filter replacement is often ignored during a tune up.
The idle air control valve could cause this problem; it it was sticking in the open position; or was not being activated.
An EGR valve that was sticking in the open position could also do this.
A defective intake manifold air temperature sensor could also do this.
An air leak at the intake manifold flange gasket could do this.
A bad fuel pump or a defective fuel pressure regulator could do this.
The use of spark plugs of the wrong heat range, or the wrong gap could do this. Many spark plugs do not come pre gapped; as they often fit different motors which require different gaps. This motor requires a plug gap of .060" (1.5 mm) and requires a hotter spark plug than most other motors. Champion # 13 or # 3013, or Autolite # 606 or # AP606 are recommended for this motor.
If the ignition switch has developed excessive internal resistance; it can cause poor cold running. This can be tested by comparing the voltage at the battery terminals to the voltage at the power wire to the coil WHEN THE MOTOR IS IDLING. If there is more than 0.6 volts difference between the two readings; the ignition switch should be replaced.