Newer Automatic Transmission Contollers?

In one of the latest 'bench build' threads, I posted a 2 door '70 Continental I saw on craigslist and my bench build for it was a newer 5.0 Coyote V8 with an auto because it's a land barge.

But on the drive into work this morning it occurred to me the transmission control might be a problem in such a build. If I wanted a modern 6 speed automatic, how would it be controlled? Ford has a control pack for the Coyote but it states it's for a manual equipped car, and even if they had one for an automatic, I doubt it would actually control the transmission, right?

Would I be limited to the older electronic transmissions that has a stand alone controller? With modern cars, is there a factor module that can control the transmission on it's own? Probably not.

Can Megasquirt control modern automatic transmissions? Or do you need another aftermarket $1k controller?

Although this question is about Ford transmissions, feel free to talk about any manufacturer and their ins and outs on transplanted automatic transmissions.

TL;DR: How do you control newer automatic transmissions when swapped into older cars?

For your specific bench build, I'd look for a wrecked vehicle with the desired 5.0/AT combo to use as a donor. I'm not sure about the newest Fords, but on stuff from 96- mid 00s that I've worked on, the PCM (computer) controlled both the engine and the transmission, so all you'd need would be the donor engine/trans/PCM. Obviously, transmissions have become way more complex since then though but on older models a manual trans PCM was really more or less an Auto trans PCM with the Auto trans functions deleted.

There's a few trans controllers out there, but there aren't setups for every trans. On the other hand, if you wanted to do enough wiring, you can probably use the ECU from a Mustang or F-150 with the Coyote and an auto, as that should run both the engine and the trans.

With Ford's, all auto tranny control is done by the PCM. Use a complete Coyote PCM/engine/transmission assembly from an automatic car.

Well that sounds a lot easier than I was fearing. What with all of the different modules you hear about and running CANbus.