1. How should the Bentusi be worked in? They don't control any planets, yet are too important to be left out.

The Bentusi could be pre-destruction of their kind? You could have them work up to creating their harbor ship as an end-game tech. Unfortunately, without planets of their own I doubt you could have the race present.

2. Should the Beast be a random event or should they be a Dread Lords-type civilization?

The Beast should be a random event- a very dangerous random event. This may be too complex but they could possibly destroy the Bentusi in the process?

3. Turanic Raiders: Major Civ, Minor Civ, or Pirate replacements?

Major civilization, make it more interesting with more playable races.

4. Should the Taiidan Republic be a separate civilization, or the Taiidan Empire's rebel faction?

You could put both in and then edit the section for race-race relations (one of the data XML files) so that if you play either race you can expect appropriate dialogue.

5. Do you want me to include Homeworld style ships (made in the Ship Builder) or would you rather create your own styles (like in the normal game)?

The one thing that really drives a mod is how in depth the you can change the game. This will be the most time consuming portion of a Homeworld mod but I think it would be well worth it considering the different types of ships from the game.

Have fun!

Why not using the Bentusi as a somewhat powerful and rare anomaly? Once you reach one, it can give you techs you can't have otherwise, lots of RUs, [or just a random speach from an unknown and unimportant prophecy to make you really really angry?]