Hi,
I'm not sure this makes complete sense. You said this was a 3.9 efi conversion. AFAIK all 3.9's had hotwire injection, this would be the 14 CUX ecu and lucas hotwire air flow meter. Can you post a photo of the ecu and air flow meter, that should tell the tale.
If you do have a 14cux ecu, the tune select resistor is wrong for non-cat tune.There was never a blue tune select resistor for the hotwire system. I can only conclude you don't have a 3.9 injection system or somebody has been messing around with it.
Ignoring all of that and anything to do with lambda control, the basics are present and correct - fuel, spark, BANG! At idle, you say all is good then when you open the throttle you get over fuelling. So you need to look at things that tell the ecu how much fuel to pour in. Air flow meter is primary input. Throttle position would be next together with engine speed. Other potential culprits could be coolant and fuel temperature sensors.
If you don't have a hotwire air flow meter I can't help you as I don't know how to test the early flapper units. Next, throttle potentiometer, carefully check the wiring and the connector, then get the multimeter out and check the throttle pot for resistance and scaling - I have posted how to do this so do SEARCH.
Temperature thermistors can again be checked with a multimeter, check the resistance values. If you want to fool the ecu, bridge the connector with a paper clip, ecu will think engine really hot so won't add any extra fuel by way of cold start enrichment.
How's your ignition system? Check the ecu has a good clean run input from the coil, comes off coil negative. Is the ignition timing correct? You might want to think about maybe doing some other mechanical checks/tests and I would say maybe look at vacuum gauge test and a compression test. This will indicate if there are possible issues with valve train.
HTH