I'm here!!
I did the 2nd gen. BP swap in my MX. There were a few wiring issues that I had to tend with like you, and seeing as how you have pretty much the same motor as me (imported jap. motor) here is what I did to get her running right:
1. ECU: I used the "BPVR" ecu. Now, you don't have to use this ecu, but you need to use a BP ecu. Using the B6 ECU will make it run like s---/no fuel economy. The BPVR ECU is used with a 4-wire o2 sensor, though only one of the 4 wires goes to the ECU. It just reads the 4-wire better. I am using a 2-wire o2 at the moment which the BPVR can run as well, but I did notice using the 2-wire it idles high until at operating temp.
2. EGR- There is no EGR on the BP.
3. Fuel rail- The fuel rail is definitely different. I had the following on my fuel rail:
[VICS]----[INJ 1]---[INJ 2]----[INJ 3]----[INJ 4]---- [harness connector]
Now, This leaves out 2 crucial pieces that were in the B6 harness (can't tell you for sure about the DOHC harness though.. only the SOHC). These are the FPR Solenoid wires, and the Water Thermosensor wires. The other, and probably biggest issue for me, was that the injectors were all on their own wire. Now it seems like they have the injectors sorted out (most likely using the B6 fuel rail) which will work, and if they are using the B6 fuel rail, you'll need to wire in the VICS. VICS was NOT part of the MX wiring harness, and was BP-specific. But pretty much the VICS goes like this:
[ECU pin 2S, the 4th pin from the left on the largest of the plugs]---------- [VICS]-----------[Fuel INJ relay.. the white/red wire]
Now, that's the VICS wiring. I'm not going to tell you about the injectors as your car wouldn't run if they were not wired up. But the FPR solenoid is pretty much the same as the VICS. 1 Wire goes from pin 2T (the pin right underneath the VICS pin) to the FPR solenoid, and the other goes to the white/red wire to the Fuel INJ relay).
Now, you'll also need the Water Thermosensor. This is pretty simple. 1 Wire goes to pin 2Q (if i'm correct it's a black/blue pin.. it's the 2nd pin from the right on the larger harness), and the other goes to ground input on the ecu (2D on the ecu).
now I'm noticing you want to use a SOHC harness for the BP. That is what I am using. Just follow the above steps to get the VICS, FPR, and Water thermosensor to work. Everything else is plug-and-play.
Really the only thing missing on the RS harness is the VICS. If your using an RS fuel rail harness then you'll only need to add in the VICS and lengthen the Water thermosensor so it reaches the sensor.
Hope that wasn't too confusing. If it is let me know and i'll clarify.
4. Intake manifold
This can be annoying, and I DO NOT recommend using the JDM intake. As you have noticed, the throttle body is different, and the 2 plugs are different. You can try sourcing the connectors for it, but even the RS harness does not have those styled connectors. On top of that, the throttle body is shaped slightly different, and so you can't really just swap out throttle bodies. What I ended up doing was swapping out intake manifolds for one off a Ford Escort GT. The Escort GT's throttle body works perfectly with the RS wiring harness, and plugs right in!
hopefully this all helps!
pic of my 2nd gen BP installed:
