The early E40Ds had problems that have all been remedied. Contact ATO transmission in Sacramento if you want a source for an E4OD that can take punishment. I can point to several Gen 1 Lightning trucks in the 9's and 10's on modified E4OD transmissions. Reason for going away from the E4OD is cost mostly...they aren't cheap.
That said, if you unplug the transmission harness from the EEC harness on that truck, you'll get a check engine light (probably) for transmission output temp, as well as missing solenoids. Depending on the year, the possible malfunction tests vary. Some of the very early trucks had no malfunction tests for transmission related failures so you might get lucky. In any case, you can buy a custom chip from any number of tuning houses to change the transmission type to manual trans. Or, if that particular year truck ever was sold with a manual trans, I'd be willing to bet you could drop in a manual trans computer and solve the problem that way as well.
The other thing to look at is where the truck gets its speedometer information. I believe that year used a speed sensor on the differential housing; but I could be wrong. If you want the speedometer to work, you should think about that in advance.