Gen IV+ ECMs are very picky, you cannot take an 07 OS and put it in an 09 ECM, it will brick.
If you use the factory 09 Express Van OS plus E38 and matching T42 TCM calibration, you should be fine. You need to use a pedal and throttle body compatible with this ECM OS as well, otherwise you'll have a dead pedal.
You can take the 6L Express van OS and retune it for your 5.3, as long as the engine has the proper 58x/4x reluctor setup.