Note: All of the following could be wrong but I think it's right. Any clarifications/corrections would be cool.
IAC thing. It's kind of hard to follow as I can't find complete diagrams of either setup but with some imagination I think I can see why they're the same difference.
I was able to find the diagram for the standard megasquirt idle control here
. It's a little more than halfway down and to the right.
Looking at that, for the "mustang" way, you can cut Q20 and D8 out. R39 is not a resistor so imagine that as just a straight line to ground.
So basically you've got a transistor that I believe is acting like a switch. The Collector (top of Q4 in that diagram) goes to "idl", which is pin 30 on the db37 (if you scroll down that page a little more you'll find the DB37) and connects to the IAC. The Emitter goes directly to ground. I'm guessing then the Base goes to the cpu then ("Idle-1") through r19 so that when the Base is energized, the Emitter and Collector become connected, effectively pulling the Collector to ground. Assuming the other wire to the IAC is just +12 from ignition, we're using Q4 as an on/off switch for the ground side of the IAC.
The last bit of the "mustang" instructions is to install a diode with the cathode (striped end) on the +12, and the other end (Anode) on the "lead that goes to megasquirt", which is that same pin 30 on the db37 that goes directly to the Collector of Q4.
So it looks like the MSnE way connects the Base in the same manner.
The Collector is wired the same way.
The Emitter is different in that it goes to R43. I did some digging and found that R43 also goes to ground, so it's really not effectively different than going to R39, especially since the MSnE have no resistor at R43.
So, our wiring of the transistor is functionally identical.
Now look at the diode. Basically instead of having it up at the IAC valve, it's down here by the transistor. The Cathode is going to the s12 pad which I found out gives +12, and the Anode goes to the Collector of Q4. On the "mustang" way the Anode goes to the wire, that in turn connects to the Collector of Q4. So it's essentially the same thing, just on a different spot along the wire.
So the only real difference I see is that in the mustang way, the +12 for the flyback diode comes from the +12 wire going directly to the IAC, where the MSnE way gets the +12 from the s12 pad.
I don't know if one is more ideal than the other.
I'll try to make sense of the other jumpers you asked about when I get more time.