Yes the computers are together because the tranny is completely computer controlled. One way to take care of that is to run your 460 fuel injected and use a F250 or 350 computer/harness to run the motor and tranny.
Go to this link
http://www.nloc.info/forum/forumdisp...e=&forumid=452 and talk to Gregg Evans. He's a Ford tranny specialist and knows the E4OD inside and out. That link is to his forum on the NLOC web board.