Car runs rough at first startup?

Recently, we noticed that the "o/d off" light flashes from time to time, and the car idles a little high to reving at a stop light, and when driving, it seems to buck off and on. We were told that it doesn't appear to be a tranny problem, but the computer reset, possibly from a dead battery, so that is no help either. Thje car rides fine and then, it runs rough, like stated above. If we shut the car down, and then restart it, the problem is gone, sometimes for the day, others for a few minutes. What should we be looking at if not the tranny?
Thanks.

I just did a head re-work because the head gasket in #2 cylinder was leaking into the water jacket. Now the eng runs rough. It ran better before the head re-work.

Engine start, run rough, then stall

Need more info. Engine size. Sounds like it may have a vacumn leak, Standing on the pass side of the engine, look down on the upper pleneum, there is a l shaped vac. Nipple that is bad about rotting away and leaking. If it is bad you can check it by temporarily pluging the port off. If it runs now and idles you have your problem, go to the parts house and tell them, or show them what is left of yours, they should have it for around 3 bucks. Thanks for using 2CarPros

9 months ago; after 500+ highway miles, car begins to miss and hesitate and slow down; only jerky throttle response; service engine soon light on; idles OK; pulled over and shut off 10 min; on restart, ran fine for to destination; replaced fuel filter, put in fuel system cleaner, sprayed Mass Airflow Sensor with recommended cleaner. Car ran fine on return 700+ mile trip and thousands of miles around down. Flash forward to this week. Essentially the same thing happened after 400 plus high speed miles, but service engine soon light was flashing, and car would barely run. Shut off for a few minutes, and it ran another 200 miles OK; set 305/306/171/174 codes; next day after 100 miles, same thing. Then, around town, running ragged. Replaced fuel filter again. Ford dlr said fuel volume and pressure within specs and cam sensor OK; wanted to replace cats for $2500+ as his diagnostics said they weren't reacting correctly; said maybe mass air flow sensor too. Independent tech found small vacuum leak. Car is running perfectly at the moment, but I'm afraid of being stranded. Because of erratic nature, can't believe it's cats. This must be something simple. TPS? Mass Air Flow Sensor? Coil packs?

Car runs fine first thing in the morning. If I drive and then park for about 20 min to an hour, and then start the car again (by now it is at operating temp), the engine runs rough and sounds like it may stall. After 4 or 5 min. Engine seems to run fine again.

Had basic tune up (plugs, rotor and cap, new wires, new air filter) but still does this.

Any ideas why or how I can fix this? Do I need a new ignition module? I hear these could be a problem when they get warm sitting near a hot area of the engine?

1995 Ford Taurus SHO 3.2L Automatic.

So I acquired this car recently from a relative and found it often either runs rough or wants to stall out all the time. Apparently my relative had this problem with the car as well. I'm pretty frustrated and tired of throwing money at it at this point, and would REALLY appreciate some advice!

What I've done so far:
1) New fuel filter.
2) Tested fuel pressure, it's OK.
3) New air filter.
4) New Throttle position sensor (because it was such a cheap and easy thing to try)
5) New EGR Pressure Switch (because it threw an engine trouble code, code gone after replacement).
6) Checked EGR system, seems to be working correctly.
7) New O2 sensors (because it threw an engine trouble code, code gone after replacement).
8) New Ignition Control Module (because engine was throwing codes 215, 216, and 217).
9) Checked all ignition system connectors for corrosion, none was noted.

Now after all that, the engine continues to throw codes 215, 216, and 217. The plugs, wires, and coilpack were replaced not long ago by my relative in an attempt to solve this same problem. I could try throwing a new coilpack at it, but I have a suspicion that's not the problem. Today I noticed that the engine is PARTICULARLY prone to the running rough and attempting to stall when the transmission is in Drive, 1, or 2. This doesn't seem to happen when it's in Park, Reverse, or Neutral.

Some other things to note:
1) The engine usually seems to run fine when it's idling in park in my driveway. However it does sometimes start to run rough and I have to keep the RPMs around 2000RPM for several minutes to keep it from stalling.
2) The car has sat for around a year without being used. I suspect the gas is stale, and I'm trying to run it out of the tank since I can't seem to be able to siphon it out. But since the car usually runs fine at idle, I'm not sure if this is even an issue.
3) ABS light is on, but I'm not concerned about the ABS system.

So my questions are:
1) What, if anything, should I try to do about the codes for the ignition: 215, 216, 217? Should I try a new coilpack? The only other ignition components left are the Crankshaft Position Sensor and Camshaft Position Sensor. I find it strange the car will usually run fine but is throwing these codes.
2) What could cause the car to be more prone to stalling/running rough when the transmission is in Drive?

Some updates:

I ran the old gas out of the tank, and put 5 gallons of fresh gas in. This didn't seem to make any difference.

I got the Haynes repair book for the '86-'95 taurus, but the book doesn't cover the ignition system used in the SHO. I found the Ford Windstar from the same era uses a very similar ignition system.

I tested my coilpack based on the specs in the Windstar manual. The secondary resistance of my unit seemed out of spec, so I got a new coilpack from Autozone and the new one matched the spec. I replaced the coilpack and the engine still ran like complete crap for several minutes, but then moderately improved after it warmed up. I used the dielectric grease on the terminals.

At the time the engine was running fair, it still seemed to miss every so often. No failure codes are returned now, so I guess that's at least progress! Where do I go from here?

I have a 94 Ford Taurus 3.0 with 142,000 miles that has been running real rough lately. The problem is it's not doing it consistantly and I am not getting a check engine light to get the codes pulled. I have taken the egr valve off and cleaned that, but that didn't work. Also what is strange if I start the car and it is running rough all I have to do is turn the car
off and start it back up. After doing this it will run fine. Do you have any suggestions for me.

Thanks!

My car does not want to run when the gas is applied. It started to just cut off coming to a stop or when I slow down. Now it when I mash the gas lightly it sputters like it is eather too rich or lean. I have not noteced no black smoke that I can tell, but I am working by myself so its hard to mash the gass and look at the same time. I think it is a sensor but I am not shure which one it is? Let me know what you think.

I have a 1999 Ford Taurus SHO with 3.4L V8 engine. Yesterday the car started for about 2 minutes then died. I took it to shop and they stated it is running on 3 cylinders and the Fuel Pump was good. They suggested taking it to the ford dealer. I drove it home today. It will start but idle is up and down. Idle is from 1,100 rpm then down to 200 rpm starts to die then picks up again at idle. When putting in drive wants to die. Well whats up with this? I do know that engine pulls a 1518 code and I have never fixed that. Idle has always been rough because of 1518 but would not start. Now starts and has eractic idle. Ideas? Thanks.

Just yesterday I replaced the spark plugs and wires and intake gasket on a 99 Ford taurus. 3.0 DOHC. When I started it back up it started to jump and back fire. I rechecked the sparks plugs and wires and the valcumn hoses and they were fine. I can not find the answer to this problem. It was not doing this before I did the tune up. Can I get some help. Thanks