This is all too straightforward. Ford planned all of this. The only plot question of this season so far: Are Ford and William on the same side?
I don't think Ford planned all of this. Ford planned some of it, but there are things going on that he wasn't involved in, either because he didn't know, or didn't care.
One of the best episodes so far, and no coincidence it had zero Delores and Teddy.
I do not believe the brain cube is Ford's, nor do I believe Ford ordered Bernard to go retrieve the brain cube and kill the humans there. I think someone else was ordering him (or perhaps his own choice? motives unclear)
I am also unsure if William's immortality project and the "get all data on all guests" project are related at all. Charlotte's desire to get whatever is locked away in Delores' dad's brain we are assuming is the "guest data" database. Since the encryption method on that file was the same as the encryption on the brain cube, if those two things aren't related, they are at least owned by the same party. How close are William and Charlottes goals? Obviously William is more concerned with personal discovery and self worth, and Charlotte more business driven...but a young William was different than the current William.
Too much speculation...just like with Lost, pointless to hypothesis as writers are probably making this up as they go. Really fun stuff though.
*Edit* Now that I think about it, I guess the "guest data" and the immortality project are probably one and the same, since the labs dedicated to both endeavorers were very similar, the encryption method on both were the same, the guest data might help to create the overall image of the mind/memories they are recreating as the brain cube.