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In modern cars a whole heap of control modules talk to each other on the CAN buss (Control Area Network)
The Auto trans has an associated control module TCM, and the ECU talks to this, as well as dash, stability control ABS steering control and much other stuff.
If you remove the auto trans and associated TCM then the current ECU is going to get upset as it can no longer talk to the TCM.
And the manual need to get the clutch switch input to start car and other stuff.
you may be able to flash the equlivant manual rom into the auto ECU eg a ZA1JB01C rom instead of the ZA1JB01D rom.
BUT their may actually be hardware changes in ECU or in wiring and the DASH VSC ABS or any other control module may need updates as well to be able to talk to manual software in ECU.
you cannot just swap in another ECU as the eCU/DASH/imobilier module are part of a security set and either need to be swapped in togeather with a key fob or re-coded by dealer (or maybe locksmith)
My guess would be it would be a very expensive and frustrating excersise to swap auto to manual. without even considering the physical fitment issues of the new transmission.
Be far easier to use a manual car for the swap.
Unless you can find a guru who knows 100% what you need to change
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