I've done the exact same thing.
1. I jumpered two wires at the plug for the E40d and never had starting problems. I don't remember the color codes off the top of my head. I used a chiltons book and it had a diagram of the gear selector switch on the side of the transmission. I think you could probably just pull the gear selector switch off the side of the transmission and use it as the jumper. Put the switch in park or neutral and it should work. I was thinking the switch doesn't actually do anything internal to the transmission.
2. There is a plug under the dash that will plug into a clutch safety switch if you want. I never installed a clutch safety switch as I liked being able to start the truck without the clutch pushed in.
3. starter is the same regarding e40d or 4-speed.
4. Removing the e40d computer and harness is a big job. The tranmission harness is completely integral to the underhood harness that goes to the cab and wraps around the front to the batteries and engine. Since I pulled my truck down to the frame I have removed most of the e40d stuff, but it was a wire by wire deal. and I had to jumper a lot of wires that normally run through the e40d computer. The tach, start wire, speed sensor, I think reverse lights all ran through the e40d. I haven't gotten my dash and wiring all back together so I can't comment on if I was successful. There is also transmisson wiring on the engine for the throttle sensor and a map sensor on the heater box. Like I said it's a big job.
5. For the 1st ten years of the swap I just zip tied all the e40d stuff up under the truck and left it there. I did have a flaky tach signal from time to time and finally it died. I'm assuming the e40d computer finally went bad. Otherwise the cruise, abs etc all worked fine running through the computer without the tranmission still connected.