Actually, you're right on the money there. I want to say I started maybe before "Phantoms", because I remember watching that episode with two interpretations in mind. (Took me a long time to kick that annoying habit, it's so hard to enjoy an episode first time around when you're already rewriting it in your head)

As for your time travel story... I say start on both plots ;) One will probably emerge as the one you want to use, and if not... then you've got two!