Q: 2004 Lincoln ls v6 my car runs bad when cold until it hits normal temp. The breaks are stiff during the warm up process

To identify the cause of poor operation like that you are describing, the cylinder firing patterns have to be looked at on a scope. That diagnostic reveals whether the issue is fuel or ignition related and also which cylinders are affected. Engine compression and intake vacuum should be verified to make sure the engine is basically mechanically sound. If the engine is mechanically sound, that is no sticking valves, steady intake vacuum, even compression, you have a problem in the fuel or ignition system. A possibility is partially plugged up fuel injectors, by the way. If that is the issue, or even a contributing factor in the rough operation, it’s best to remove the injectors from the fuel rail and send them to a lab (e.g., Mr. Injector). On car cleaning is not effective because each injector has an internal miniature, replaceable filter basket. Other possibilities are a vacuum leak, an air induction fault like a stuck idle air control valve or a faulty throttle position sensor, problems with the mass air flow sensor, defective spark plugs, faulty wiring to the coolant temperature sensor and so forth. If you desire that this problem be diagnosed by a certified Mechanic, dispatched by YourMechanic right to your location, please request a rough idle diagnostic and the responding certified mechanic will get this resolved for you. If you have further questions or concerns, do not hesitate to re-contact YourMechanic as we are always here to help you.