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The ECU question is easily solved with an MS3Pro PnP or MS3Pro. The PnP version will cost you $1,499 and use an OEM wiring harness. The MS3Pro will cost you $1,749 including the wiring harness. Both systems will work nicely for you supporting the VCT, drive by wire if you wish to use it, and a myriad of other features including flex-fuel capability. Both the MS3Pro systems contain a wide range of engine save features along with other nice to-have features like a wireless Bluetooth connection capability between the ECU and your laptop for tuning and data logging purposes.

With respect to transmissions go with the strongest unit you have access to which would be the 6R140. If you are using it in a truck with a hopped up engine you will need strength.
 

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Some ECUs have the transmission control logic built in, others a microsquirt specifically programmed to control transmissions. From your questions, it sounds like you are in the deep end of the swimming pool without a life jacket. If you have never done this before you should proceed with caution. The Ford strategies for a given ECU typically only support the transmissions Ford sold with the particular model vehicle the ECU was taken out of. There is some limited ability to "reconfigure " this by going to different ECU strategies but I would be surprised if you could find the code from Ford that would run the range of transmissions you are considering.

If you intend to stay with Ford ECUs you are going to need to do a fair amount of research before you select a particular transmission. If you go aftermarket you can do pretty much anything you want. Your commentary suggests you are looking for a plug-and-play solution and to my knowledge, it doesn't exist outside the transmission offerings Ford has originally provided for the vehicle. That doesn't mean it can not be done. Your commentary suggests you are unknowledgeable and unwilling to invest the time or money in learning. That pretty much leaves you with the options Ford offered for the particular vehicle you have selected.

Another item you might want to consider is the fact the aftermarket ECU's provide all manner of engine safety overrides, traction control tools, multifuel strategies, fuel metering strategies, VCT support, support for both high and low impedance injectors along with any size injector and a myriad of additional features and tooling (not to mention documentation — which Ford doesn't offer) to get the job done.

You should assess your personal skills levels in both the mechanical and electronic controls domains to determine if you believe you are up to the task of taking on a project of this magnitude.
 
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