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First you have to get the leak fixed.
Is the engine running at operating temperature? What does the temperature gauge showes?
Take your wehicle to a shop for a steering / suspension check. It may be getting unsafe to drive.
Possible blend door actuator or broken blend door link problem. Unfortunately the dash must be removed and the heater box must come out for further inspection.
I think you have bent valves due to the broken timing chain.
Try this: Get in your truck, turn the key to ON position (do not start the engine!) and within 3 seconds push the accelerator pedal to the floor and let it back. Turn the key off, than start it and see if it's working good now.
Does the engine reach operating temperature? What's the temp gauge showing after you drove it for a while? It may be just a thermostat and the CEL relates to the long open loop mode.
Make sure the electrical connector is seated in the throttle correctly. Reset the DTC and do a throttle re-learn.
It could be a problem with ignition coils or engine wiring harness. Search the net for "Nissan technical service bulletin 01-059" it explains a bit deeper.
Well, the car should stop at red lights. I guess the problem is that the engine stalls at red lights. I'd suggest a computer diagnostic. It may have an idle control or a sticky EGR valve problem.