I hate electrical problems! This may sound like a stupid suggestion however since you had both the engine and trans out of the truck, did you happen to forget the ground straps from engine to truck frame & engine to body?
If he removed the E4OD harness entirely then no amount of ground-strapping will get the starter and the reverse lights back online. See on the E4OD trucks all the wires run together in one harness, it is fully possible to open said harness and separate them by function though:
- two light blue ones (one solid and one with a black stripe) will be going to the transfer case, even if truck is 2wd the wires are there but the round 4-pin connector (white in color IIRC) they terminate into is just capped off. Keep those for reusing in a 4x4 truck, or in case a 4x4 swap is planned in the future at some point.
- bunch of wires will be going to the passenger side of the E4OD, they are loomed together and lay on top of the transmission case - grab their connector and just pull the whole bundle out of the harness, they are for the solenoid pack and have no function in a ZF5 swap, discard them all. Should be a grey connector but just match its shape to that in the trans, as it's possible the MLPS connector on the driver side is also grey but will be different shape. You are removing all of the the passenger-side wires, not the driver-side ones.
- the MLPS connector on the driver side has 4 wires that you need - an "in" from the start switch (starts as red/lightblue at the jumper under the column, likely changes to white/pink inside the trans harness tho), an "out" to starter relay on the fender (red/lightblue all the way), and the two for the backup lights (pink/orange and black/pink). So connect the white white/pink and the red/lightblue wires together and that should give your start function back. Then the pink/orange and the black/pink wires should be extended and spliced into a connector for a manual transmission backup switch - Ford used the same connector on everything from the '70s 4-speeds all the way to the end of the OBS trucks, also said connector is available aftermarket as it's know to break after a while just from age and heat - so find one of in your local parts store or online, splice it into the E4OD wires, and you should have reverse lights again. Once you have all these wires sorted out, discard any others that are now dangling loose
This is all for the bricknose trucks as that is the EVTM we have right now, good chance it applies to the OBS trucks as well but do some wire tracing and proving just in case.
Additionally, if one is to remove the E4OD TCM entirely from their truck, or simply power it down by removing its relay, it is likely the tachometer on the dash will go dead. I can provide the fix for that (again you simply connect two wires together) later tonight as IIRC the colors were not quite what the manual suggest they should be so I'll need to double-check on that.