Essentially, once you're past Alternate Earth, nothing's missable, right? I'm trying to get some of the 100% achievements (namely treasure chests and quests) and don't want to screw up now that I'm about to hit disc 2.
First, there are four rapier recipes that you'll need to learn ASAP if you want the 100% Item Creation achievement.
Second, after you finish the story events on Roak, there's a quest that involves going into the Astral Caves to help out some knights. In the second room, there's a knight on the ground near the entrance, and talking to him triggers a quest.
I've heard that if you don't activate (and possibly complete?) that quest before completing the main Astral Caves quest, it's gone.
Third, while not technically missable, if you sell the SRF Protector before making it into an Iron Protector, or the Iron Protector before duplicating it for a shop order later on, you'll have to hope that the Wandering Dungeon gives you another SRF Protector. It's better not to leave that to chance.
Related to that - you'll get a Laser Weapon from a quest late in the game. Don't do anything to it until you have the Duplication skill and can make a backup copy. Again, you can get more in the Wandering Dungeon, but why leave it to chance?
Finally, if you want all the Battle Trophies (by far the most time-consuming achievement), it's useful to make a backup save after returning to Aeos. There's a save point right before the part in question, so when you reach a save point, make a save that you're not likely to overwrite.
That's all the major stuff I can think of. Overall, there isn't that much to worry about for the 100% achievements once you're at Roak, other than actually filling all the shop orders and making all the items. (Both are time-consuming processes. Getting all the chests isn't too bad if you keep track of the ones you've already gotten, though.)
Dragon Fogel, Marquis Elmdor's Arch-Nemesis. Don't call me "Dragon".
There are a bunch of excellent guides on x360a that I use, you should try them out
I was using that site for most of my information, but there were several little mistakes and wanted to be sure.
But anyway, got the 100% treasure chests achievement and just have the Wandering Dungeon shop quests to finish for 100% quests, too. Also managed all the endings, although I had to use a few love potions for Meracle's (and by extension Crowe's).
Nearly done with this game. I've got four items left to create for the 100% item creation, all of which involve Ethereal Queen's Feather. I managed to beat her once, but it took practically all my revival items and a lot of character swapping. Definitely going to need to go back and grind some levels and battle trophies before making another attempt for the rest of the feathers.