For grins, consider one more KOKO (not KOJO) routine to force the ECM (computer) to re-learn the IP's position (TDCO re-learn) just in case the ECM swapping cleared it out:
> Starting from Key 'Off' and engine cold (169F and cooler), simultaneously floor the fuel pedal (APP 100%) and turn the key to 'Run' but *DO NOT* attempt to start. Hold this for 60 seconds.
> At the end of 60 seconds simultaneously release the fuel pedal (APP 0%) and turn the Key to 'Off'. Wait for 30 seconds.
> At the end of 30 seconds, start and drive normally.
> When the coolant (ECT) reaches 170F the ECM will trigger a re-learn of the IP's physical mounting position and the motor might 'blib' / stumble very briefly (or you might not notice anything at all). If the motor grumbles, grouses, and belches for a while, this is an indicator that the IP is not healthy. If the Check Engine light turns 'On', this is an indicator that the IP needs physical adjustment (depending on the code) to bring it back to a normal range.
Back to the point . . . While KOJO probably set the TDCO re-learn as part of your tune, the swapping might have cleared it without it occurring. Reasoning for doing the TDCO re-learn is that ECM controlls the injection timing based on load and in order for it to do this job correctly the ECM needs to know the IP's actual mounting position on the motor.
Also, doing the TDCO re-learn is necessary whenever anybody removes & re-installs the IP, so keep this in mind for future use
