I actually heard, that they released a pilot which included a new part with details of who the killer was, for Europe. And when the DVD series was released, they put this new edition as the pilot. Worst, I decided to watch the Director's Cut, with even more details.
The pilot with the alternate ending is what they call the "mind warp" ending that has a few more details and basically a lot of the things that were later covered in the dream sequence in 1x03.
I don't want to say yes or no to your theory about Bob. All I can say, very truthfully, is that it's a little bit more complicated than that.
Perhaps what you're looking for isn't released yet (season 2 aint out here either, I know because I've only seen the first seven episodes of it on laser disc. Ironic, I call myself a die-hard fan of this show and I haven't been able to see all the episodes). But stillI wouldn't go out and read the spoilers yet. It's worth the wait to see the twists and the answers to the mystery played out in Lynch's vision.