My crank blew out a thrust washer at 20007, currently in the process of tearing it apart.
The ECM from the 03 will work with the 07 engine as long as you move the headers from your 03 to the 07 (assuming both are XB9 blocks, that should be bolt-on; the xb12 has a larger diameter)
The starter and all that junk will work fine, and yea if you use the same intake bits (airbox and such) from your 03 and just swap the engine block and such itself over you should be fine to fire it up and go. I would move over the injection system as well just to make sure, but I don't recall that it changed.
A lot of people were very surprised when we cut my filter open to find so much copper and iron inside, the old sportser platform (05 and newer I believe) has a really good bearing set that usually lives a long happy life