The fids are also the playlists. Some of the fids are playlists, others are music files.

The database files get rebuilt on-the-fly when you synch (instructions to synch after copying the files are in the drive upgrade guide).

Copy the ini file whenever you like. At any point after the new drive is fully built.

But you don't really need to copy the ini file unless you've got a lot of handcrafted custom stuff in there. Mostly, the ini file stores settings in the "Configure Player" screen in emplode, so it's better just to go in there and fix up the settings there after you're done.