The injectors on the 3.8 and 2.9 are both batch fire set-ups meaning they are all wired together. What I read was three were hooked to one injector and the other three were hooked to the other. Yoyu will have to run an EGR for the 2.9 and the sensors from it too. As for the air by pass pump thing, I didnt run it seeing that the 2.9 didnt have it (from what I remember) but if the 2.9 has it then run it.
My only thing was fuel, I didnt have time to get fine tune and reduce what the engine got but had a few plans on if I did run the 3.8 setup how to reduce it (that is if I was still using it).
The only wires that were splicd into the 3.8 harness from the rangers were the three that go to the TFI moduel on the dizzy that came out of the driverside firewall. The other three were from the 3.8 harness to the computer (the three ranger ones were just T'ed into the three on the 3.8 harness) and all colored wires going to there respective colored wires since they all matched.
As for fuel pump, that is up to you how you want to run it. They say to keep it at ford factory 44psi. With the 3.8 that was giving to much fuel but thats propbably just to how the system was setup for injector pulsing and fueling.
When I ran mine, I didnt run any of the emissions stuff but the O2 sensor and then I think I didnt have it hooked up right since the 3.8 has two O2 senosrs that had i think 2 wires each so that may have caused a few problems too and the ranger only runs one with one wire.
I will say that it started right up everytime, had nice power ecept whn you got on it hard du to it over fueled the engine making it sluggish and blow out black smoke (looked like a diesel sometimes). I also had a high idle hangging problem too since my 3.8 setup came from an auto tranny and what happened there was after reving up or letting off the gas it would hanmg around 2000rpm anywhre from 2-12 seconds but my fix was using the throttle accutaor thing. I just unplugged it and used the adjusting screw for it to set my idle to 800rpm and left it unpluggd or my prioblem would rturen and it would try to set the idle elsewhere. But if you find a manuakl tranny setup for a 3.8 it might be better or if you have an auto tranny it may work out in your favor. Try to find the set-up from the same tranny type that you have, 2.9 might be easier to find in what you are looking for and I dont know how an auto computer from a 2.9 will act with a manual tranny.
The worse that can happen, you will return to the Duraspark set-up or if you dont wire stuff carfully, short something out on the fuel injection systm but careful wiring will help avoid that.
Sorry to be long winded but this is my experiance (and lack of) with bot the set-ups.