What do I do when I hit 99?

[Rustic]

This is one case where Abyssea hoses new players.

Yeah, you hit the level cap. You have minimal gear, no Gil, and your skills bite, hard. On the other hand, now you get to skill up. A lot. Offhand, I'd do it while leveling a few more jobs, like SAM or WAR for your DRK, SCH or BRD for your WHM, and probably Ninja somewhere in there as well. It'll likely let some of those defensive skills go up in the process, and depending on how cruddy you've been, some of your spellcasting skills as well.

-Don't- level them all the way up in Abyssea-style exp alliances. Do some solo GoV/FoV, then some GoV parties for a few levels, then solo again to give your skills a chance to catch up. In the long run, you can't avoid improving your actual skills, regardless of level.

(And this sorta situation is why L99 newbies exist- and shouldn't. Yeesh.)

[Mirage]

I'm not sure what missions to go do...

All of them. You could start with your nation, then go on to RotZ, then whatever you want.