PoE is still run, it's good, VoG is irrelevant these days, motes of light give experience on your equipped gear to unlock upgrades, strange coins are still useful, exotic shards are really useful, motes of light are also useful for the same reason as exotic shards (upgrades), unless you have The Taken King you can't level up any further, you can infuse Year One guns into Year Two guns if the Year One guns have higher attack, they didn't really change the raids but added two more, everything is for The Taken King now since they took off all our Heroic and Nightfall strikes as well as all but three Crucible modes, and faction reputation is gained via getting something called a Faction Allegiance for 2500 Glimmer from the Faction Representative and then earning Vanguard and Crucible rep which will go to your Faction rep instead.
EDIT: Just saw you got The Taken King. With what you have, I'd reccomend getting some Year Two exotics this Saturday from Xur, which will put you on a good start. Then run some PoE and some high-level strikes, and you should be fine. Make sure to do every The Taken King quest you now have availible, as those are geared towards people coming from Year One to Year Two and give out good gear and XP.