From spare part manuals, I found that main wiring has different part numbers:

749s 2005

510.1.390.1A - front wiring
510.1.391.1A - main wiring

749 2003

510.1.243.1A - front wiring
510.1.256.1B - main wiring

749 dark 2005

510.1.391.1A - main wiring

But, from this ducatiforum thread it seems that the ecu are swappable.

Even better, it seems that the immobilizer works in different way in newer ecu, so just put the correct firmware seems to “virginize” the ecu.