No mention of year. Assuming the same as a '99, the CLU is under the driver's seat and the ECU is in the trunk. Separate items. The CLU sends a code to the ECU to start/run.
The CLU checks your key against the code in the EEPROM, if good then sends a code to the ECU. The ECU is re-programmable so you possibly could have the new one programmed to your CLU. Going the other way, you can take the EEPROM out of the new engine's CLU and put it in yours but then you also need the key programmed.
You do not have to change the ignition switch as there is no affect on starting. It is only a coil and interrogator that reads the pill in the key. Even with a push button start the CLU needs to have the pill code sent from the ignition switch.
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