The 4wd trans that comes with the 3.5 EB is either 6 or 10 spd automatic. So, now you can't use the Ford Motorsport control pack, you need to use the control module out of the vehicle you pulled the engine out of.
And the control module is linked to the ABS, and Electronic stability control. So, now you are wiring and reprogramming an automatic transmission, ABS and ESC module. And they need reprogramming because unless you are putting the drivetrain into something very similar in size/dynamics i.e. Rust's '79 F-150, you "fool" the sensors which can lead to really bad things e.g. instead of ESC preventing rollover, it causes rollover. As a result, the aftermarket has been slow to venture into this market - you have to figure out how to delete all electronic nannies without harming rest of drivetrain.
Reverse engineering takes time and money, so there needs to sufficient market that wants (can afford) a 3,5EB rather than say 5.0.