I have a 99 Taurus that runs rough?

I replaced the heads and water pump and the car was running great for about 100 miles until I was driving and it just shut off. I couldn't get it started. The fuel pump was working and I checked the coilpacks all good, no spark at the plug. Replaced cam sensor and crank sensor still nothing. I found a wire that goes to vehicle speed sensor rubbing against heads and appeared to short out. I took to ford and they said computer was bad, I replaced with used one and it ran rough, ford said to let it run and it might recognize the unfamiliar new home and run ok. It still running rough and using alot of gas. Do I need to have comp flashed?

To add to what "Stdyhand" said, you also want to make sure the calibration sticker is the same on the used computer as it is on your old one. You should have had the codes pulled first with an OBD2 code reader before throwing money at the car.

No you don't need to replace your car. I'm willing to bet your computer wasn't bad. It amazes me how anyone that works around cars all the time is so quick to blame the ECM. All the years I've been working on cars I've seen one PCM that was bad.

First question is do you have a check engine light on? If so, what are the codes? The fact your using a lot of gas would point me to a bad sensor. No spark can also be caused by a bad ICM. Sometimes the car will even run with a bad ICM but it will run very rough. I would have it tested at least. Make sure it is grounded well when put back on. Clean your MAF sensor with CRC Mass Air Flow spray. Do NOT use carb cleaner or brake cleaner. A bad ECT and O2 sensor can cause a car to run rich. A bad fuel pressure regulator will cause the car to burn rich. You will likely see black smoke from the exhaust and smell raw fuel.

Without knowing any codes all you can do is just troubleshoot the problem. I would start by testing fuel pressure at the rail. If you have 30-40 psi your likely ok and I would skip to making sure all plugs are firing. If their not make sure the plugs and wires are good, check coil resistance, ICM, etc.

Do a compression check and make sure all cylinders are within spec. You said you replaced the heads so it is very important to make sure you have proper compression after doing a job like that. If compression, fuel, and spark is good I would start by R&R all sensors.

ONLY after doing all this would I start to look at a PCM. While a computer has been known to fail, the chances compared to the problem being something else are very much slimmer.

I had one of those cars - don't put anymore money in to it. I was in the shop at Ford on a regular basic.

It is time to replace the car.