They are getting cheaper all the time, but for now you're better off using the 4.2 you know is good aren't you.
AFAIK the auto boxes are the same, the 4.2 might be valved a little differently, for economy perhaps but if you keep the 3.9 box it's more than up to the job and it might work out a bit faster that way :D
If you want to stay with the 3.9 I'll swap you for the 4.2
Anyway, the electrics. I was sure that the post 1990 wring loom swere all the same, but a mate has been looking for the lambda plugs on his and they don't appear to be there, so you might need to swap the loom. As it is the loom doesn't unplug, you either need to remove it form the engine or from the ECU and feed it out through the bulkhead, which might be easier if you don't fancy messing with the mutlitude of plugs on the engine.
Either way you want the ECU from the LSE or an upgraded chip like the RPI Tornado. The LSE ECU will probably be set up for running Lmabdas and I don't know how well they run without them, but if you don't fit them you need to change the Tune Select Resistor near the ECU for the one that's in now.