I guess since I started this thread, I should have to list my answers too.

1.
As for ranking their careers, I go:
1a. Barrera
1b. Morales
3. Marquez

Maybe I'm taking the easy way out by putting Barrera and Morales in a tie, but that's the way I feel about it, I don't think you can really say that one was definitely better than other. I think they go into history as equals. I scored their trilogy at 1-1-1 (Draw in the first fight, Morales winning 2nd, Barrera winning 3rd).
When someone mentions Barrera, they're always going to mention Morales, and vice versa. And that's the way it should be.
If Barrera had convincely beaten Marquez, I would have had to put him as #1 all by himself, with Morales #2.
I have a lot of respect for Marquez, but he doesn't have the number of big wins that the other guys have. I know he was the victim of bad management decisions, but Morales and Barrera spent their entire careers fighting the best. You can't penalize Barrera and Morales because Marquez didn't get the big fights until now.

2. If Marquez beats Pacquiao, I'd have to consider moving him up the list, but he would have to absolutely destroy Manny. If he wins a very close decision, I would still rank him slightly below Morales and Barrera.

3. I think Morales would have beaten Marquez in their primes. Very very close fight, but I like Erik in that matchup. Shame that it never happened.