Good news on many fronts.
Picked up my new to me 4D34-2AT3A injection pump today, as well as the corresponding ECU, a number of sensors, and injectors. I also picked up a second 2AT injection pump that is in rough shape simply as a core if I ever need a pump rebuilt, or as a learning piece to tear apart and experiment on.
I also received my complete 96-01 Fuso OEM service manual covering ever model (FE, FK, FG, FM, etc.) within that year range.
After reviewing the service manual for the 97 FE (that I pulled the pump out of) and the 99 FE (that my current engine is out of), there are ZERO wiring differences on the transmission side of the circuit. Yes, the connectors are different, the trans themselves are different, and the TCUs are different, but as far as inputs/outputs and required sensors, there are no differences.
The 2AT truck still has a throttle position sensor on the throttle pedal in the cab, and its sole purpose is to provide pedal position to the TCU, it isn't even wired to the ECU.
Speaking of the ECU, it is much much smaller than the 3AT ECU, and much simpler. There are only 47 pins total, and only about half are used. The only thing the ECU reads is RPM, Coolant Temp, Boost Temp, Pre-stroke position, and it ouputs pre-stroke controls accordingly. It also has a tach output. The plugs on the pre-stroke portion of the pump are the same, so I can still use those portions of my current engine harness. Re-wiring will simply be a matter of finding the correct pins at my current ECU connectors, and soldering the connections to the new ECU connectors.
The 2AT service manual also defines what each screw on the pump does... one for idle RPM, one for may RPM, and one for fuel rate. Pretty simple. The governor accounts for boost mechanically and is actuated by a throttle cable.
I am genuinely excited about the downgrade/upgrade, and will document thoroughly including pictures once I get it going. I think the trickiest part will be fabricating a bracket onto the OEM pedal assembly that will allow the TPS to mount up and function.