I'm wondering why it would be cheaper to change the entire engine instead of just the internals.
The swap would require a new transmission, drive by wire, and probably to complete electronics, not just the software. Plus the entire swap is pricey as hell.
If you go with the internals, I would only guess that modified software would be needed. And the install should be cheaper than a swap. I'm just guessing here.
Headers and pulleys are no-brainers, and cams can be installed by any halfway competent shop with the right tools.
Only thing I imagine to be really pricey, is if the ECU needs custom software tuning. Other than that, I can't imagine an internal swap to be physically or financially more complicated than a complete engine/tranny/electronic swap. As said I have no experience with this stuff, and only know as much as I read on forums...
It may be cheaper to just FI the engine, or change the car for a 330ci/i.