I had the same symptoms in my EB and it turned it to be a dodgy throttle position sensor, although I don't know if the battery would have any impact on it.

My old 94 EF falcon has been having issues with rough idling and rough gear changing after having a new gas converter fitted. We changed coil packs, spark plugs, leads, sensors and put in a new computer. The only things we hadn't changed were the idle control and the map sensor and the idle speed sensor.

BUT today after disconnecting the battery to reset the computer after fixing a leaking air intake pipe the car was running worse, rough and lurching into gear and not changing properly or idling properly. I have read through these forums and decided to pull out my Haynes repair and maintenance manual that I bought 17 years ago and see what else I could work out for the problem.

I stumbled across a section by accident that said..." Throttle position calibration". Reading on, this is basically what it said in general information...."Whenever the battery is disconnected the transmission must re-learn the closed and wide open throttle positions to enable the PCM to determine the proper gear to select for the apropriate throttle position"

I followed the simple instructions in the book and recalibrated the throttle position. It took about 15 minutes to do and was very simple and required no tools or code readers etc.

Not only did it fix the rough gear changing it also fixed the rough idling. My car now no longer runs like a chaff cutter and the gear changes are the smoothest they have been in years.

I told my brother what I found and what I did and he was stunned. He has worked in the automotive repair industry for over 30 years and he had never heard of doing this before now. He said I taught him something today.

So if anyone has an old Haynes manual for EF falcons you can find the instructions in section 7B-4. Hopefully you solve your idle and throttle control problems like I did.

if anyone has a copy of this section ... could they share it?

I attached two documents which are copies of photos of the manual and the section. I couldn't upload them as JPG because they were too big. Hope they work. If not I will find some other way of doing it.

thanks for the try, they didn't work. if your able to ... send them jpg's to me & i'll post em.

I managed to reduce the size of the photos. Hopefully they aren't too small now.

 

 

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Here is a close up of the six steps to calibrate the throttle. Its is spread over 2 pages.

 

 

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What you are saying is nothing new, but clarify what you mean by the engine running like a chaff cutter, if you mean a bad idle yes, but missing under load would have absolutely nothing to do with disconnecting the battery.
Disconnecting the battery the ecu will loose it's random access memory there fore the idle speed control motor would have forgotten how much air was bypassing the throttle plate before the battery was disconnected.