Any tips for item management? How do I know which equipment is safe to sell? Do I store the innocents first? There's like a trillion item categories, how should I sort them to get a semblance of order? And is there some easy way to optimize equipment, or know when it's time to shop for more?
When you have so many items and can get more easily, it doesn't make a lot of sense to do all that innocent management. The ones you should pull out are statistician, broker, manager, mentor, instructor, and professional. Those give boosts to XP earned, money earned, that sort of thing. And even then you should only keep maybe 8-10 of each, because you won't need a lot more once you unlock the Innocent Farm and can breed them.
Generally do not sell rare or legendary items. Many of the unique one-time-only items are legendary so following that rule will stop you from getting rid of them. Often quests will ask for a number of rares or uniques to turn in so you will be glad you kept all those rare low level fists etc.
Start by selling duplicates of any item that has the same innocent in it, like if you've got two of the same sword with gladiator in them. You could make it a goal to only keep 2 or 3 of every item type on hand...I'm sure pros at the game just sell everything low level though.
To sort items just go to the main page displaying all of them and hit X. It'll be fine, they'll all line up in order of power and it will apply to the other categories too.
The best time to upgrade your equipment is always the start of a new chapter, that's when the shop upgrades. You could do it every other chapter.
Wow that seems like a lot.
Are there any must have classes for beginners?
The sage is basically required for very late end game stuff. It has a spell that hits every unit on the field, however for much of the game this will be useless and do no damage because its power is very low, you need crazy boosts for it to work.
Gunners and pirates are fun. Oh also wrestlers for throwing people all over the place. But really play as whoever you like.