Just replaced head gaskets and timing chain

Please elaborate on "hard to start". It cranks too slowly? It backfires? It cranks normally but won't run? Was the battery disconnected? How does it run above idle?

Go out and drive it. Tthe Engine Computer lost its memory and has to relearn "minimum throttle" before it will know when it must be in control of idle speed. It also will not give you the normal "idle flare-up" to 1500 rpm when you start the engine. To meet the conditions for the relearn to take place, drive at highway speed with the engine warmed up, then coast for at least seven seconds without touching the brake or gas pedals.

It's not that it doesn't recognize the throttle position sensor. It's that it doesn't yet know what the lowest signal voltage is that it will send out at idle. All throttle position sensors are different and not adjustable. For training purposes we always say they are fed with 5.0 volts, and there are mechanical stops inside it that limit the signal voltage to 0.5 volt at idle to 4.5 volts at wide-open-throttle. In reality, you may find 0.38 volts at idle with one sensor and 0.46 volts with a different one. The exact value isn't critical.

If you install that second sensor that provides 0.46 volts at idle, the computer already has that 0.38 volts in memory from the previous one. When it sees the new 0.46 volts, it will "know", (incorrectly), that you have your foot on the gas pedal so it will leave the engine speed up to you. It will not try to maintain idle speed until it knows your foot is off the gas pedal, and it knows that when it sees 0.38 volts.

The same thing happens after disconnecting the battery. There is no default voltage value because half the time it would be lower than what the TPS actually delivers at idle, so it would still have to relearn the new value. There has to be a way for the computer to know when your foot is off the gas pedal. It knows that by a high vacuum reading from the MAP sensor. The problem is you could snap the throttle open briefly in the garage. When you release it, vacuum will go real high as the engine slows down, but that still doesn't prove you fully released the throttle. To address that, the computer needs to see that high vacuum for at least seven seconds along with a steady voltage reading from the TPS. The only way for that vacuum to be real high for that long is by coasting, and coasting with a TPS reading that is steady and not bouncing around proves your foot is off the gas pedal. THAT'S when the computer looks at the TPS voltage and puts that value in memory. From then on, whenever it sees that same voltage, it knows it has to be in control of idle speed.

If you install a new TPS with a lower voltage at idle, the computer will recognize that and learn that as the new minimum throttle. If the new TPS voltage is higher than the old one's, it won't relearn it until you do the coasting procedure.

That 0.5 volts to 4.5 volts becomes important when talking about diagnostic fault codes. The only way for the signal voltage to go to 0.0 or 5.0 volts is with a break in a wire, a break inside the sensor, a loose or corroded connector terminal, or a wire is grounded. The throttle position sensor is strictly a mechanical device so it can't really send out the wrong signal voltage that is still within that acceptable range. A MAP sensor sends out the same range of signal voltage but since it has a lot of circuitry inside, and since it has a diaphragm that can have a pinhole leak, it IS possible to send out the wrong voltage that is still within the acceptable limits. Suppose at a certain load on the engine the voltage corresponding to the manifold vacuum is supposed to be 1.3 volts. The computer uses mainly that reading to calculate fuel metering. If the sensor reports 1.6 volts instead, the computer will act on that and deliver the wrong amount of fuel, but it will not set a fault code because 1.6 volts is an acceptable value, even though it's the wrong value. That's how you can have a running problem with no fault codes. Eventually the oxygen sensors will pick that up but all they will do is report a lean or rich condition. You still have to diagnose why that condition is occurring.

If you have a misfire, that can be the cause of the low idle speed and stalling if the computer doesn't see it and respond fast enough.

Look at the "AIS steps" on your scanner. That is usually under "Sensor Data" even though the automatic idle speed motor isn't a sensor. It can also be called the "idle air control" valve. As it opens, it opens a passage around the throttle blade to let more air in. At the same time it increases the length of time it holds the injectors open. Those two things control idle speed. The computer can place that motor in one of 256 positions. For a properly-running engine, step 32 is typical. With a single cylinder misfire, you'll find it at around step 50. That valve has so much control, I saw a Chrysler trainer disable six cylinders on a V-8 Jeep, and it was able to maintain the correct idle speed on just those two remaining cylinders.

If you find the AIS on step "0", either the computer hasn't relearned minimum throttle yet, or it thinks the idle speed is too high and is trying to fully close the valve. It reduces the injector pulse width too to all the cylinders. A vacuum leak will cause a high idle speed, (without the corresponding increase in power), and that reduction in air AND fuel to all of the cylinders by the computer can result in an excessively lean condition and a lean misfire.

If you find the number much over about 32, it recognizes the idle speed is too low and is trying to correct that.

If one cylinder is responsible for the misfire, switch the spark plug and wire or coil with those from a different cylinder to see if the misfire moves to that new cylinder. You can also switch the fuel injector with one from another cylinder. If the misfire stays on the same cylinder all the time, that leaves compression as the problem, or something is wrong with the computer or wiring going to the coil or injector. Computer and wiring problems are the least common causes of a misfire, and a compression problem won't be intermittent.

When you can feel a misfire, that is because the rotational speed of the crankshaft slows down slightly during the missing power pulse. That change in rotational speed is what the computer detects and what sets the misfire fault code. Since it knows when that happens in relation to which plugs and injectors it's firing, it knows which cylinder is responsible. It just doesn't know why.

You can also look at the oxygen sensor readings to get some clues. If you see the right bank is always lean, suspect a misfire on the passenger side. If you also smell raw fuel at the tail pipe, suspect a spark problem. There's obviously plenty of fuel but the mixture is not being fired on one cylinder on that side. Oxygen sensors don't detect fuel, just oxygen, so a failure to burn the mixture in one cylinder will result in unburned oxygen being detected by the sensor and unburned fuel being smelled at the tail pipe.

For the low idle speed you can remove the idle speed motor and check inside the passage to see if it's plugged with carbon. That was more common on the 3.0L engines years ago. Haven't run into that lately with the better additives in the fuel.

The rough running is due to a misfire, and up until now the assumption has been the two symptoms are related. If there's no codes, look at what you have for "AIS steps". If it's still "0", whatever is causing the misfire may be preventing the minimum throttle relearn from taking place.