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There are two things on the EF that cause this
1. is the inhibitor switch or gear position switch - it tells the computer what gear you are in as well as preventing starting in gear. If it is faulty the ecu doesn't know what to do.
2. Is the Throttle position switch, if this is faulty the computer drops into kickdown and flares the engine or drops into limp mode.
Thats the most common causes in my experience. I imagine the new gearbox came with a gear position switch fitted so I'd go for the throttle position switch (TPS)
4000 rpm is still very high even with the power option in.
I have an EF and an AU and worked on countless falcons. I have never experienced gear changes that high unless the throttle was very hard depressed.
If you are only on half throttle the changes should occur much earlier.
This may get better with a bit of driving with one driver as the computer learns the driving style of that driver.
After the gearbox change it will be a relearn but this usually takes only around 30 to 50kms.
Ok this usually indicates a problem with the information getting from the TPS to the ecu and down to the transmission. It can be a TPS (throttle position switch) problem.
In which case remove the wiring plug on the TPS and spray the contacts with a contact cleaner - this may help but if the TPS is faulty it will need replacing.
OR - It could be an ECU problem - can be replacd with a second hand one but ...
TRY checking the harness down to the gearbox, give every connection a wriggle and a open and clean, a loss of even a tiny voltage over a dirty connection can cause problems.
Check that plug into the gearshift position switch again.
Try going for a drive with the TPS disconnected if its the same then that will be the cause. Under $100 on ebay.