I don't think it's a big deal to change to the newer engine. I know of an E46 saloon getting an LCI 35d engine fitted, so if that can be done what you're asking should be a cakewalk.

Don't ask me the specifics but I have it in my head that there is some differences in the electrics, but nothing major.

Fully dressed those engines will still fetch pretty big money with low mileage and even then you don't know how it was driven or maintained when it was in use.

Personally I would be much happier knowing the cars original engine had a new lease of life.