Questions on swapping in new ecu

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Senior Member
Heres my current setup (the way it was when i bought it):

PR3 OBD0 5 speed ECU
Mugen fully re-mapped ECU chip
No rev limit
Disabled governor
Disabled both O2 sensors, oil pressure, and knock sensor

Im planning on tuning with s200 and p28 ecu. My question is will swapping in the new ecu basically change evrything to the stock settings and enable all the sensors, oil pressure, governer, etc? Are all these controlled by the ecu?