I break 'sessions' up into threads, so session 1 would be Chapter 1, session 2 would be Chapter 2 and etc.
1) This is something I do in my Real Life games as well, and i find a suprising amount of people prefer not to spend their destiny points, saving them for the much loved 'Cheat Death' or the dramatically appropriate use of a Pheonix down. Also, I only give Destiny Points when I think I deserve it rather than at the times the book suggested, so if the party rolls over a boss monster, I won't give them the destiny point but if they survive a harrowing encounter I might give it to them instead, so it's a choice between 'use it for a relatively small boost of power now, or save it for when I actually need it later.'
2)The five point limit break is also something I do in my real life games. As they can only trigger on a use on a natural 12 on a 2d6 roll and the expenditure of 3 destiny points (1 point with the Limit Breaker ability) I see no reason why a hero, even if starting out, wont have at least a small one. The way I see it, this relatively small limit break simulates the hero putting his/her upmost effort into trying to defeat their enemy and using everything they've got.
Not to mention the fact that leveling in play-by-post takes a while and having something small to tide the players over until they get the full thing help that a little.
3)Everyone will gain their full ability scores and skill points by the end of the intro.