chances are the plug is already there. there is a bypass installed for the E4DOA trucks. stripping out the in cab harness is prolly not necessary. the clutch switch will be needed though. i generally bypass mime.
In other words, he does not need to do anything with the clutch switch, just leave the jumper in place in his old harness. That's what I would do also.
There is a plug underneath the brake booster area. There is a short harness that goes to the transmission. Unless the factory changed this, you can unplug the harness from the zf 5 speed and it's transfer case, unplug your old e4od harness, and plug in the zf harness in the plug under the booster. The zf harness will have the jumper inside it to jump out the old neutral safety for the e4od.
As far as all the wiring for the computer controls for the e40d, I would hope that is separate and comes right out, but maybe not, I have never messed with a e4od.