Make sure you get a Fuel Injection Pump Lever (FIPL) from the side of the IP when you source the transmission. It works like the VRV and vacuum modulator on the C6 trucks
I had my VRV rebuilt by Nick P. on Ford Trucks Enthusiast forum. His name is genscripter there. I don't know if he's on OBs. Here's his website.
DIY Repair for the 6.9 and 7.3 IDI Diesel Van (and other vehicles)
www.nickpisca.com
I think you can buy a FIPL new at the parts store. If you don't have one that is properly adjusted you'd have to use a fully-manual valve body. I'm not even sure if those are available for the E4OD. I considered it briefly for my C6 but had the VRV rebuilt instead.