Start with testing the throttle position sensor. It is the most suspect here. If needed, they aren't particularly expensive to replace. Here is more...
The cruise control issues is most likely not related to your transmission shifting problem.
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The throttle position sensor is connected to the throttle shaft on the throttle body. It sends throttle valve angle information to the PCM. The PCM uses this information to determine how much fuel the engine needs. The TPS is really just a simple potentiometer with one end connected to 5 volts from the PCM and the other to ground. A third wire is connected to the PCM. As you move the accelerator pedal with your foot, the output of the TPS changes. At a closed throttle position, the output of the TPS is low, about a half a volt. As the throttle valve opens, the output increases so that, at wide open throttle, the output voltage should be above 3.9 volts. Testing can be performed with an electrical meter. Analog meter is best. You are looking for a smooth sweep of voltage throughout the entire throttle band. While slowly opening and closing the throttle, take note to the movement of the voltmeter needle. There should be a direct relationship between the needle motion to the motion of the throttle. If at anytime the needle moves abruptly or inconsistently with the movement of the throttle, the TPS is bad
You should have 5 volts going into the TPS. At idle, TPS output voltage must be greater than 200 millivolts. At wide open throttle (WOT), TPS output voltage must be less than 4.8 volts.. The best is to use an analog meter (not digital) to see if the transition from idle to WOT is smooth with no dead spots. With your meter set for volts, put the black probe on a good ground like your negative battery terminal. With the key on, engine not running, test with the red probe of your meter (install a paper clip into the back of the plug of the TPS) to see which wire has the 5 volts. One of the other wires should show .26V (or so). The other wire will be the ground and should show no voltage. Move the throttle and look for smooth meter response up to the 4.49 at WOT.
Perform the test procedure again and wiggle and/or tap on the TPS while you watch the meter. If you notice any flat spots or abrupt changes in the meter readings, replace the TPS.
The TPS is sensitive to heat, moisture and vibration leading to the failure of some units. The sensor is a sealed unit and cannot be repaired only replaced. A TPS may fail gradually leading to a number of symptoms which can include one or more of the following: -
NOTE: The throttle position sensor is also DIRECTLY involved with transmission shifting characteristics! It should be verified early in the troubleshooting process, when a transmission issue is suspected!
Poor idle control: The TPS is used by the ECU to determine if the throttle is closed and the car should be using the Idle Air Control Valve exclusively for idle control. A fault TPS sensor can confuse the ECU causing the idle to be erratic or "hunting".
High Idle Speed: The TPS may report faulty values causing the engine idle speed to be increased above normal. This is normally found in conjunction with a slow engine return to idle speed symptom.
Slow engine return to idle: A failing TPS can report the minimum throttle position values incorrectly which can stop the engine entering idle mode when the throttle is closed. Normally when the throttle is closed the engine fuel injectors will be deactivated until a defined engine RPM speed is reached and the engine brought smoothly to idle speed. When failing a TPS will not report the throttle closed and fueling will continue causing the engine to return to idle very slowly.
Engine Hesitation on Throttle Application: The TPS is also used by the ECU to determine if the driver has applied the throttle quicker than the Manifold Air Pressure sensor can read. The fueling is adjusted acordingly to cope with the sudden increase in air volume, however a faulty sensor can cause the ECU to ignore this data and the engine will "hesitate" when applying the throttle. In extreme cases with the engine at idle, a sudden application of full throttle can stall the engine.
Engine Misfire: A fault TPS can report values outside the deined acceptable range causing the ECU to incorrectly fuel the engine. This is noticable as a slight misfire and can trigger the misfire detection software and/or Malfunction Indicator Lamp (MIL) light on the dashboard. Extreme cases can cause excessing misfires resulting in one or more cylinders being shut down to prevent engine and catalytic converter damage.
