they are always listed alphabetically by title, with the play order incrementing consecutively

This is because you don't have the track numbers in the file names. This is covered in the FAQ, here.

2.0b3 you could "drag and drop", within the right hand window, to re-order tracks.

It's Alt-drag now. This is covered in the same FAQ entry as above. There is a bug when you do it, though, in 2.0b7. If you've previously checked the "delete these tracks from the player" box, it will delete them when you drag them, so watch out.

Personally, I don't like the fact you have to alt-drag now, I liked it better without the alt-dragging. But at least now you know how to do it.

with the HTML stuff, and it accepted it. The tracks were visable under the tracks/genres etc branches on the left tree view, but I couldn't access/find the root directory I added to move it.

This is by design.

Anything you drop onto the player goes into the soup views by default, no matter where you drop them. The root page was specifically coded to accept drops for this very reason.

Eventually, the Soup views will be playable from the player's main menu, and all of your artist/album trees will become unnecessary. The default way to add tracks to the player will be dragging them onto the root page. Creating playlists will only be needed for special things like "mood" playlists.