when are you refreshing haunt? when the spell itself is on cooldown or when the debuff falls?
affliction is also fairly dependent upon when you use your cooldowns (hint, very often). Nef is also probably a bad fight to judge DPS on also b/c of all the downtime between phases. Do you have any logs?
Also, when you apply CoD can be very important, you want to try and put up CoD when you have spell effects like power torrent and/or trinket procs up. I can't see your armory, but if you don't have a Dark Moon Card: Volcano yet, you should get one. They're still BiS even in heroic firelands content (well... 2nd BiS, Rune of Zeth is BiS... it's stupid).
How I do my rotation:
CoE -> Shadowbolt for crit -> haunt -> UA -> Corr -> shadowbolt again unless all my procs are already up, then CoD -> back to shadowbolt -> haunt whenever it comes off cooldown -> UA when duration < 3 secnds left -> shadowbolt.
Below 25%, drain life + haunt when it's up, but don't clip a drain life short, wait for it to tick, then haunt, but hit haunt as close to "on cooldown" as possible.
If there's two targets that you're soul swapping between, then switch from CoD to CoA, since CoA can be on multiple targets but CoD can't (the tooltip is misleading on this point).
I guess always make sure fel armor is on? lol I know that sounds dumb but sometimes I'll be doing a 5 man or something going, "wtf why is my dps so low?" then realize that I haven't had fel armor on.
Can you maybe post here what spec you use by using wowhead since armory is down for maintenance?