Question: What exactly was Clu's vision of "the perfect system"?
Question: In the first movie, Kevin was seen being digitized and sent into the Grid. What caused Sam to be sent into the Grid?
Answer: Same exact thing. He used the same machine that digitized him in the 1st movie. You can see the same machine in his secret computer lab.
In the first movie, a laser shot out and digitized Kevin so why didn't it happen again when Sam got digitized?
Well, it's been 28 years since Flynn first visited the Grid, so he's either updated the machine so it's safer or it's a simple visual deviation from the filmmakers.
Answer: Sam and all the other familiar faces were just programs that looked like people we knew. Flynn was the only user actually in the computer world.
Question: When Alan meets with Sam, he tells him of a pager number coming from the arcade Kevin had but, the number hasn't been used in twenty years. Who activated the number and why?
Answer: CLU activated the number to draw Alan, or Sam, into looking for Flynn, where they'd discover the computer and reopen the gate, so that CLU could escape into the real world.
Question: Tron fought for the users, so how was Clu able to make Tron serve him?
Answer: Because Clu was given all the authority of the most important user, the creator, Flynn.
But what did Clu do to Tron to make him serve him? Tron fought for the Users so it would make no sense for him to suddenly side with Clu who wanted to create the perfect system and help him in annihilating the ISO's.
When Clu and co. attacked Tron and Flynn, Flynn's disc must have been damaged, removing his personality in a way similar to amnesia. This allowed Clu, now master of the system, to gain control of Tron's skills. Later, when Prinzler saw Flynn, he remembered him and what he did, and regained his original purpose.
The answer was in the movie itself. During a conversion between Sam and his father it is mentioned that Clu had the ability to repurpose programs. This is the action that allowed him to "build" the perfect system. The isos were manifested without creation from anything and had genuine freedom that Clu couldn't repurpose. This is why he destroyed them because it threatened his strategy to create perfection. Answer: Clu repurposed Tron to serve him and do his bidding. That simple.
Question: During Clu's "Toast" to his army, there is a closeup of one particular program that has been converted. For some reason, this looks like Gem to me, even though the impression is that she died in the End of Line club (though if the sequence happened in real time, there was plenty of time for them to escape the club before it blew) Is it supposed to be Gem, or another significant program, or just a cool shot showing Clu's reflection in the visor of the program?
Chosen answer: There's no indication that it's anyone we'd know. I'm pretty sure the shot was simply placed there for the visual it creates.
Question: After Rinzler "destroys" Clu, Flynn suddenly develops the urge to switch disks with Quorra. Why? As far as he is concerned, Clu is dead. He has no reason to think otherwise.
Chosen answer: He doesn't know Clu is dead. And a little prudence never hurts. Flynn knows Clu and clearly it was entirely possible that Clu was still alive. If they all got back to the portal, it made no difference. If Clu showed up to stop them, Flynn knew what he had to do and needed to make sure that Sam had his disc to get out.
Answer: Going by Clu's behavior and personality in the film, Clu's idea of a perfect system was likely a system where every component worked as intended and as expected. One where every action by programs could be consistently predicted. The Isometric Algorithms very existence went against everything that he believed was "perfect", in that by their nature their actions could not be predicted. Users also seem to exist in contrast to Clu's beliefs as their human emotions cause them to act irrationally and erratically.