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(Mark VIII) MKVIII "Flash Tune" and Manual Transmission options


Well-Known Member
GOOD INFO AT www.ffcobra.com
Here is a detailed write-up by "Domino" regarding PCM configurations when using a manual tranmission with a MK VIII donor. Also included is a mechanical change needed to do the manual transmission swap that some may overlook. Hopefully this will help others in the integration of the Mark VIII 4.6 DOHC engine and PCM to a F5 manual transmission roadster

Information for 93-95 Lincoln MKVIII donors with the Ford EEC IV PCM.

If you eliminate the auto transmission and switch to a manual transmission, there are a few mechanical changes needed and multiple options to choose from with regards to the integration of PCM electronics.

First, be aware that the Mark VIII DOHC has a 6-bolt crankshaft requiring a 6 bolt pattern 4.6L SOHC flywheel. The 4.6L DOHC Cobra has an 8-bolt flywheel and will not fit.

One overlooked additional requirement that has been discovered when using Ford Racing Performance Parts (FRPP) flywheel and a FRPP clutch assembly, is that you will need to be certain to purchase the diaphragm clutch bolt kit part #M-6397-A46. This includes the dowel pins that align the diaphragm properly and eliminates clutch chatter and engine vibration. These pins are NOT included with the flywheel or clutch kit. They have to be purchased in addition to them. If using an aftermarket flywheel and clutch assembly, be sure that all bolts and dowels that are needed are included. Also remember you have to install a pilot bearing in the crankshaft for the transmission input shaft.

For those who want a manual transmission and plan on using all emissions equipment and PCM from the early MKVIII you will need to rewire the neutral start/backup lights connector to work with your manual transmission. If you do not re-wire the connector the car will not start and you will not have any back up lights (if installed) If the connector is bypassed properly, the PCM will not set any codes and the starter/back up light circuits will function normally.

A basic diagram of the wiring needed is attached below.

Please note that wiring varies year to year. Please refer to your correct year EVTM manual if your connector/wiring varies.

For further clarification, the back up light wires will need to be connected to the back up light switch on the replacement transmission. The starter wire terminals in the connector will need to be jumped.

For those desiring to delete the auto transmission and other emissions components from the PCM you will need to purchase an add on "tuner chip". At the time of this writing, Chris at I squared (www.isqe.com) can get the chip and have it custom flashed to remove your specified components for $450.00 including the custom performance tune. The Detail Zone (www.thedetailzone.com) can also perform this service for $350.00. Both these options are a one-time service. If you decide to change anything in your build later on, you will need to send back your chip and have it reflashed for an additional fee. This option still retains the EEC IV PCM and will still troubleshoot according to the factory diagnostics procedures.

Those desiring the ability to flash out any unwanted emissions items, change to manual transmission, and plan to upgrade various engine components in the future may want to check out a Tweecer (www.tweecer.com) chip/programming software setup. For this system you will still need the EEC IV setup from your donor but will add on a chip that has a connector for hooking up to a laptop computer. The software is available for windows only at this time. Through their software and laptop interface you can "flash out" any unwanted equipment, and make any changes you desire to the fuel map/spark tables. Please note it was not known if the data-logging feature at time of this write up was able to work with the MK VIII PCM. This part of the software is used to determine if changes made while tuning were a benefit or loss, and is used to diagnose MIL on conditions and other drivability issues. At the time of this writing, it is unknown if the Ford diagnostic procedures will still be effective with this system installed. An advanced knowledge of engine fuel/spark programming may also be needed when using this setup to performance tune the vehicle.

For those desiring OBD II programming and diagnostic capability, you may consider purchasing a 96 MK VIII PCM and wiring harness setup. The Detail Zone carries an aftermarket wiring harness specifically for the MK VIII DOHC engine that allows a Ford EEC V PCM from a 96 MK VIII to be used with the early MK VIII engine. Please note that in order to flash tune this setup you will need to either send in your PCM to I squared, The Detail Zone, or purchase a SCT, Diablosport, or Sniper Tuning programmer to be able to custom tune and flash out unwanted items.

When deciding between programmers, research and consider these items.
Will the programmers allow you to re-tune if you add performance items in the future or is it a one-time program only?
Will the programmer allow you to also use it as a scan tool for diagnostics?
Does the programmer have a data-logging function for extended diagnostics?
Your needs on this will vary.

Also please note that the PCM from a Mustang Cobra that does not have Coil on Plug ignition may work with this setup as well. However, custom tuning of the spark/fuel tables may be required due to differences in cam/intake manifolds.

You can also custom build your own wiring harness by using a 96-99 Cobra or 96-98 MK VIII Main harness and the early MK VIII engine harness. If you decide to do this, you will need the EVTM manuals from both vehicles, as some wiring is not the same from one to the other. This includes items such as the knock sensors, ignition coil circuits and the intake manifold runner control system circuits.

It has also been suggested that the later style coil on plug Cobra PCM and applicable harness system may be used. If you cannot find a used PCM, auto parts stores including NAPA and O'Reily's can order a remanufactured PCM. They will add a core charge that you “may†be able to eliminate with a Mark VIII PCM. Some parts stores will allow you to exchange a PCM from a different vehicle for the one needed if it is still a EEC V computer. Make sure you ask before doing this.

Please be advised with any of the above options care must be taken to make sure all wiring connections are accurate and modifications to the harness/connectors may be needed for proper engine operation.

The most flexible setup is the aftermarket stand-alone engine management system. There are a few available that will work with this setup.

So far the least expensive is the Megasquirt system. Cost varies as you can purchase this as an electronics kit that will require soldering together. Some suppliers carry it as already assembled. There are also other options for the Megasquirt setup that you may or may not need depending on your application. This system has been proven to work with the DOHC modular engine, however; it will only batch fire one bank of injectors (all four on one side of the engine) at a time and will not provide for a sequential (individual fuel injector) firing for more precise fuel tuning. As of this writing, Megasquirt was developing a sequencer to allow for sequential fuel injection but it is not available yet. A projected date is March 08 so check back.

AEM performance makes a universal stand alone engine management system that will handle sequential fuel injection with either the stock early style 2 coil pack (Ford EDIS) system or the newer Coil on Plug system. It was also suggested that 034 Motorsport (www.034motorsport.com) Stage IIC stand alone system will work as well, if using a Coil on Plug setup. These are only just a few of the options out there. Many other manufacturers have stand-alone systems available. Note: These systems will require custom integration of their wire harness to achieve proper engine function. These also can be extremely expensive depending on manufacturer. Also, with some stand-alone systems an advanced knowledge of engine fuel/spark programming is needed for best performance.

Hopefully, the above information I have provided will help others trying to mate a manual transmission with a Mark VIII 4.6L DOHC donor.

Dave aka “Dominoâ€

We all should thank Dave for taking the time and effort to research what is becoming a popular transmission choice for many F5 builders with Mark VIII donor cars!
Good Job...!



Well-Known Member
I am able to start the car by jumping the starter, but I am not able to start it with the key. When I jump the starter it runs fine as long as I have the key on of course. I switched to a t-45 and I am thinking it is something to do with a neutral safety or something of that nature. I am still running the Lincoln computers and wiring.


Well-Known Member
I have a mark viii engine from a 98 n it has coil on plugs, can I still use a gt harness that has the coil on plugs?
I started with a mark 8 and a gt harness from a 97 we had the car running there is a link on here for the cop conversion is actually pretty simple,as long as you pay attention,which I did not the first time:banghead:.


Just read through that. So many options. What are you guys doing with emissions components? Leaving everything that came with the donor or deleting some or all?


Well-Known Member
Staff member
I like to use the emission stuff, just because I don't know where the car (or me) might end up in any given year.