I know you cant go whenever you want, because I could not do it when i got to the third disc (After I went into the crater atleast). I had Yuffie with me, no matter how many times I went in there, the Turks wernt in that cafe, and Yuffie never stole my materia. I remember that for a FACT, because when I went to do the Turtle Paradise flyer quests, and I went to the island, nothing happened at all, which was also around after I beat the game (Saved right before I went into the crater). So there IS a certain point where you cannot do it, I just dont know what it is. Maybe when the Weapon destroys that village, or when it comes up to Midgar.
As for Aeris' final limit break, all you need to do is get the Mythril from the dude in that cave and give it back to the weapon seller and pick the chest upstairs. The one downstairs is some piece of crap armor I think.