So after reading your post eleventeen times, i have concluded that you are doing a 4x4 swap on your E-550 using parts from an F-550. You yanked the transmission and transfer case from the "truck" and installed it in the "van" but now you have shifting issues because one has a "gear" driven VSS and the other has an electronic VSS with a trigger wheel?
That said, you want to know if you can swap the ECU from the truck into your van in hopes of curing the shifting problem with the 4R100 without having to purchase additional components that might cure the issue?
The simple answer would likely be NO. You would have to study the entire pinout on that ECU to verify that the trucks are wired identical, the gear ratios are the same, the engines are the same, the gauges are the same, all the sensors are the same, etc... The odds of the ECU pinout being the same are slim and none.
Im still confused on what it is your doing with the pitman arm. I can only conclude that your existing pitman arm doesnt match with the "trucks" draglink taper?
Just blink once for yes and twice for no....