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Start by checking the coolant level make sure it is not low and repair any leaks. Check the fan clutch and make sure it is not wet with oil on the front of it indicating it is bad. I would replace the thermostat it sounds like it is sticking. If its not the thermostat clean the radiator fins sometimes they clog with dirt and debris. The water pump could also be defective make sure you are getting good coolant flow through the system.
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Here is the code definition:
Diagnostic Trouble Code (DTC) P1299 indicates an engine overheat condition was detected by the cylinder head temperature (CHT) sensor. An FMEM Strategy called Failsafe Cooling was activated to cool the engine. (Refer to Section 1A, Electronic Engine Control (EC) System , for more information on Failsafe Cooling Strategy and the cylinder head temperature sensor.)
Is the engine coolant level fill correct?
The vehicle runs rough because it is cutting off injectors in order to cool the engine. I would double check and make sure the vehicle is not overheating.
If you are absolutely sure the truck is operating at a normal temperature and the cylinder head temp sensor is new then there are only 2 more things it could be. A concern with the wiring harness or connector or a processor concern. Check the harness for any chaffed wires grounding out against a metal bracket. The pcm is the absolutely last step because there is no way to test it other than replacing it.
Where is the pcm located? Is that the one under the kick panel?