Not much I can say here. I've seen these cutscenes so, so many times.

"Let's go get Mascot" they say. Ha ha ha. Sorry but you'll have to keep waiting a bit longer for that.

I recommend doing Chapter 5 out of order, partly since the guide expects you to go to the Via Infinito smack dab in the middle of it (which is not gonna happen) and partly because some quests are better done over a longer period of time - the Ruin Cave especially; if you encounter any chocobos during your other quests make sure to catch them, and if you have any in your ranch might as well dispatch them now to save time later. Oh and make sure to dispatch one disposable chocobo to Bikanel, you won't regret it when the time comes to dig a lot.

And of course as long as you do everything there is to do you'll still reach 100%, even if you don't have the convenient checkpoints along the way.