Timeless Isle is the primary thing to do once you hit 90. This will pretty much get you outfitted with everything except weapon and a single trinket. Depending on how lucky you are you will get a burden or two. Download the handy notes plugin for timeless isle, helps make sure you get all the chests open. Try and hit up / tag celestials for a small chance of 553 legs / hands.
Depending on your class, look at the 553 crafted waist / leggings on the AH. They are usually pretty good and give a quick ilvl shot to balance out some lower items. Also check out the crafted weapons that are available. I was able to get a 502 2h for my DK when I hit 90 as someone was selling it for cheap.
Make sure to turn in your charms for warforged seals and start burning them on bosses that drop critical pieces of gear, weapon is generally the biggest for DPS types.
I found this link useful for gearing up.
FAQ: I'm a fresh 90, how do I gear up? PATCH 5.4 edition : wow
Getting 496 is probably the first goal for SoO, but getting a good weapon and around ilvl 520 should be quick after it. At that point you can get in on Flex. From my limited experience, Flex is easier, saner, and a better experience than LFR. You do have to know the fights though which can take a week or two of LFR. There are also new mechanics to read up on.