I feel your pain. I initially only changed a few shortcuts, then a few more, then a few more, and now it’s to the point where I find it insufferable to try to edit with anything but my own set.
As for the upload/download dialogue box, I always assumed something like that was supposed to show up, but for me it never has. As I primarily edit on 2 machines, both of which I am the only real user, I haven’t really needed to do this frequently. So I gave up on it pretty fast and went with my old familiar way of copy/pasting prefs.