Interesting points.

I thought that Clemenza was responsible for Vito's safety. If I remembering correctly, there was a scene, another one I think was used in the longer Godfather Saga tv edit, where Sonny retrieves his father's address book from his safe and calls Tessio because he thought that Clemenza may of had a hand in his father's assassination attempt.

As for Sonny's murder, we can see Tom ordering bodyguards to follow Sonny as he races off to see his sister.

One thing I wondered about was the scene in Part II where after the botched assassination attempt Michael tells Tom that he's going to be the Don in his absence. I always thought, given Michael's manipulative nature, that he fed Tom the line about thinking of him as a real brother in order to play on Tom's fears that he'd somehow let the family down during the Sollozo business.