Very strange misfire, Help!

I have just finished putting a 91 motor into my 86GT. The motor is bone stock save for longtube headers. Now the problem is that I have a bad miss on cylinders 1, 2, 6 and 8, it is so bad that the paint on the new headers on these cylinders is still black and has turned light gray on cylinders 3, 4, 5 and 7. I hooked a timing light to each individual plug wire and you can visibly see that there is a very bad miss, sometimes it will only fire once every few seconds. I have tried changing TFI modules, distributors, cap, rotor and still nothing. I am very puzzled because of how dramatic the difference is between the cylinders that are firing and those that are missing. After running for a few minutes you can grab the header tubes that are missing while those that are firing are burning hot.

Also there is a random orange wire near the back of the intake, where should it be going?

The car still has the stock wiring harness, computer and speed density setup.

Can someone please help? I am thinking that the next step may be to change the computer? Bad ground somewhere? ANY suggestions would be greatly appreciated!
 
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The random orange wire is the O2 sensor heater ground. Bolt it to the back of the cylinder head or intake manifold to eliminate possible O2 sensor problems.

Dump the codes and look for a code 14, PIP sensor fault.

Dump the codes and see what the computer says is wrong…Codes may be present in the computer even if the Check Engine light isn’t on.

Here's the link to dump the computer codes with only a jumper wire or paper clip and the check engine light, or test light or voltmeter. I’ve used it for years, and it works great. You watch the flashing test lamp or Check Engine Light and count the flashes.

See Troublcodes.net Trouble Codes OBD & OBD2 Trouble Codes and Technical info & Tool Store. By BAT Auto Technical

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If your car is an 86-88 stang, you'll have to use the test lamp or voltmeter method. There is no functional check engine light on the 86-88's except possibly the Cali Mass Air cars.

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The STI has a gray connector shell and a white/red wire. It comes from the same bundle of wires as the self test connector.

89 through 95 cars have a working Check Engine light. Watch it instead of using a test lamp.

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The STI has a gray connector shell and a white/red wire. It comes from the same bundle of wires as the self test connector.

There is a single dark brown connector with a black/orange wire. It is the 12 volt power to the under the hood light. Do not jumper it to the computer test connector. If you do, you will damage the computer.

What to expect:
You should get a code 11 (two single flashes in succession). This says that the computer's internal workings are OK, and that the wiring to put the computer into diagnostic mode is good. No code 11 and you have some wiring problems.

Codes have different answers if the engine is running from the answers that it has when the engine isn't running. It helps a lot to know if you had the engine running when you ran the test.

Trouble codes are either 2 digit or 3 digit, there are no cars that use both 2 digit codes and 3 digit codes.

Alternate methods:
For those who are intimidated by all the wires & connections, see Actron® for what a typical hand scanner looks like. Normal retail price is about $30 or so at AutoZone or Wal-Mart.

Or for a nicer scanner see EQUUS DIGITAL FORD CODE READER (3145) – It has a 3 digit LCD display so that you don’t have to count flashes or beeps.. Cost is $30.
 
I ran the KOEO test and came back with codes 23 (tps out of range) and 81 (Air management 2 circuit failure (AM2/TAD)), not anything that is going to cause it to miss like that I don't believe... Also I did not get the code 11 when I first started? How do you go about doing the KOER test? Just hook it up the same way and start the car? I did this and all I got was 4 flashes.
 
I had the same exact problem your having. The cylinders that were missing would only fire once in a while and when they did it was very weak. It ended up being a bad distributor, which was from Autozone and only a few months old. Where did you get the distributor that you just installed? Was it from a parts store or a junkyard? If it came from a parts store or even a junkyard it should have some type of warranty with it. If I were you I would look at the distributor again.
 
I have changed the dizzys with 3 different ones and exact same results, changed the computer yesterday, same result. It seems if I unplug the MAP sensor the miss gets worse on the bad cylinders and still runs ok on the good ones... Could this be the problem? I am going to try to get another MAP tomorrow.
 
Have you dumped the codes? There could be some clues as to the source of your problem, and possibly a direct pointer to the problem itself.
 
What do the plugs look like on the missing cylinders? If the o2 wasn't functioning properly due to no ground, your plugs may be fouled. It's a remote possibility but easy enough to check.

Set your TPS position also. .99V koeo if I remember correctly.
 
I'm not even getting spark on the wire right at the distributor, could a faulty MAP sensor be causing any of these symptoms?

The MAP sensor has nothing to do with the ignition.

Here's a book that will get you started with how the Ford electronic engine control or "computer" works.

Ford Fuel Injection & Electronic Engine Control 1988-1993 by Charles Probst :ISBN 0-8376-0301-3.

It's about $25-$35 from Borders.com see http://www.amazon.com/ . Select boo...very good, and I found it to be very helpful.
 
13726548? And yes the timing is at 10* with spout connector removed. Only codes that are being thrown are o2 sensor codes as I dont have an o2 harness at the moment. Also throwing a TPS voltage code but I don't think that could be causing the miss. Anyone have a link on how to set the TPS?
 
Setting the TPS: you'll need a good Digital Voltmeter (DVM) to do the job. Set the TPS voltage at .5- 1.1 range. Because of the variables involved with the tolerances of both computer and DVM, I would shoot for somewhere between .6 and 1.0 volts. Unless you have a Fluke or other high grade DVM, the second digit past the decimal point on cheap DVM’s is probably fantasy. Since the computer zeros out the TPS voltage every time it powers up, playing with the settings isn't an effective aid to performance or drivability. The main purpose of checking the TPS is to make sure it isn't way out of range and causing problems.

The Orange/White wire is the VREF 5 volts from the computer. You use the Dark Green/Lt green wire (TPS signal) and the Black/White wire (TPS ground) to set the TPS. Use a pair of safety pins to probe the TPS connector from the rear of the connector. You may find it a little difficult to make a good connection, but keep trying. Put the safety pins in the Dark Green/Lt green wire and Black/White wire. Make sure the ignition switch is in the Run position but the engine isn't running.

Here’s a TPS tip I got from NoGo50

When you installed the sensor make sure you place it on the peg right and then tighten it down properly. Loosen the back screw a tiny bit so the sensor can pivot and loosen the front screw enough so you can move it just a little in very small increments. I wouldn’t try to adjust it using marks.

(copied from MustangMax, Glendale AZ)

A.) Always adjust the TPS and Idle with the engine at operating temp. Dive it around for a bit if you can and get it nice and warm.

B.) When you probe the leads of the TPS, do not use an engine ground, put the ground probe into the lead of the TPS. You should be connecting both meter probes to the TPS and not one to the TPS and the other to ground.

C.) Always reset the computer whenever you adjust the TPS or clean/change any sensors. I just pull the battery lead for 10 minutes.

D.) The key is to adjust the TPS voltage and reset the computer whenever the idle screw is changed.

The TPS is a variable resistor, must like the volume control knob on a cheap radio. We have all heard them crackle and pop when the volume is adjusted. The TPS sensor has the same problem: wear on the resistor element makes places that create electrical noise. This electrical noise confuses the computer, because it expects to see a smooth increase or decrease as the throttle is opened or closed.

TPS testing: most of the time a failed TPS will set code 23 or 63, but not always. Use either an analog meter or a DVM with an analog bar graph and connect the leads as instructed above. Turn the ignition switch to the Run position, but do not start the engine. Note the voltage with the throttle closed. Slowly open the throttle and watch the voltage increase smoothly, slowly close the throttle and watch the voltage decrease smoothly. If the voltage jumps around and isn’t smooth, the TPS has some worn places in the resistor element. When the throttle is closed, make sure that the voltage is the same as what it was when you started. If it varies more than 10%, the TPS is suspect of being worn in the idle range of its travel.