These are good questions, and I've formed some conjectures as to the answers.

Regarding [1]: Michael went to Cuba largely to try to discover who the traitor in his family was. But when he learned that Fredo was involved, this was for him somewhat disappointing, not only because Fredo is his brother, but also, and more importantly, because he must have surmised that Fredo could not have been the only traitor -- surely he didn't slit those assassins' throats. (As a side note, I think Michael is being honest when he says to Tom that Fredo didn't realize that Roth misled him, and that he shouldn't be afraid to come back to Nevada. In my view, it's only after Fredo says in the boathouse conversation that he helped Roth because he thought "there was something in it for him" that Michael decides that Fredo must be killed. To be duped is one thing, but to be duped as a consequence of selfishly trying to partially "break off" from the Family and have some action on one's own -- that's quite another, and deserving of the penalty dealt to traitors). So when Michael returns from Cuba, he still has some detective work to do -- who else in his family was involved? To make this discovery he must use the same technique he used earlier: Michael utters the famous "keep your friends close, but your enemies closer" remark to Pentangelli because he says this is how he'll be able to find out who the traitor in his family is. Since the Cuba trip yielded only a partial answer, he needs to employ this tactic again to find out who the other traitor was. This, I think, explains why Rocco is still treated as though it's business as usual.

Regarding [2]: This one is far tougher to answer, but I think a reasonable conjecture can be made. I believe that Michael suspected it was most likely to be Rocco at some point before the "difficult, not impossible" conversation. Sometime after that conversation, I believe Michael "tested" both Neri and Rocco -- some kind of conversational ruse, similar to what he does after the failed Tahoe hit, i.e. he goes to the two possible suspects, Roth and Pentangelli; he is almost certain it's Roth, but he still rips into poor Frankie like a lightening bolt ("IN MY HOME!") as if Pentangelli was behind the hit -- a little trick just to verify that he is right about Roth. So I think some kind of ruse like this was used on both Neri and Rocco. I also believe that Michael thought, in advance of using this ruse, that Rocco was the more likely suspect because Rocco was in charge of compound security, and he had far more opportunity than Neri did to point Michael's bedroom out to the assassins. Also, I come back to the audience's point of view (as distinguished from Michael's): Rocco hands Michael the "orange from Miami," he's wearing an orange jacket during the assassination attempt sequence; and the movie begins with him kissing Michael's hand. [edit/deleted an error].

Another point is that after Michael learns that the attempt to kill Roth failed, he knows he has to figure out a way to try again. Since Roth will be impossible to kill unless a suicide assassin does it, Michael holds off on confronting the suspected traitor with the same type of "suicide deal" he offered Pentangelli until he has an opportunity to kill Roth -- i.e. when Roth returns to the US. This way Michael gets rid of his traitor and Roth in "one stroke," as Machiavelli would say.