No the rails are not interchangeable. Go look at both head and notice the spacing of the injectors.
But, swapping tunes is as easy as loading the preferred file via the PC. You could make swapping motors as easy as you like by making the wiring harness and the fuel connections as modular as you can. Then all you have to deal with is the exhaust and intake setups.
I suggest you read a lot and check out the various vendors of MS kits and such to determine what you need to pull this off.