Try enchanting and gemming your gear correctly, If I remember correctly you stack Armor Pen. I think. But take out the stupid gems like Spell Pen...no point. Agility and Armor Pen is your friend. and also Enchant your gear. thats where alot of your dps is failing at.
Your hit is too high and you have some gems for +hit. You are using the weakest version of gems for slots that are correct ( IE +12 crit) and as Briax pointed out spell pen is of 0 use. Your 2hander stat stick is pretty weak for a hunter ( the only benifit u are getting is the arp and haste with some stam) I suggest you run Halls of Reflection for the Orca Harpoon. You are specced MM. That being said are you adhereing to the Shot priority spelled out in the Hunter guide Stickied to tthis forum? Read over it a few times. If you are not dead set on MM I would suggest trying SV and learning that, DPS is less Bow oreintated and you can see some pretty nice numbers once you learn it.
In short, your problems are in small parts with the way you finish off your gear, but more then likely larger with the way you manage your shots in combat. Gear score is a very basic intial tool to jude if someone has the potential, it does not equate into insta DPS as some seem to think.
Okay, you have many, many issues; however, with a little work and with your gear you'll be doing 4k dps in no time. The first thing I recommend is changing to a Survival spec. You have a least 2 survival spec glyph (Kill Shot and Explosive Shot - why you an Explosive Shot glyph when you don't have the talent is a bit puzzling). For your Survival Spec, copy mine on Wharfrat - it's a Vanilla Sur Spec; some can argue over Hunting Party; but until you really learn what your hunter can do, just copy mine and don't deviate because some other talent looks cool.
I recommend Survival because you don' the gear level for MM yet. Okay, as for Glyphs, keep what you have, but get rid of Aspect of the Viper and pick up either Steady Shot or Serpent Sting. I go with Steady Shot since as long as I keep Serpent Sting on my target I get 10% damage bonus. For minor glyph pick up the mend pet one, it will let you throw a heal(s) to your pet and make it happy so you don't have t to feed it all the time.
You pet spec needs some help - copy my pet spec for ChinaCat; my wolf.
Okay, gear. First off remember with a hunter - at your gear level - you want Agility, it's your number one stat; every red socket should be Agility; every yellow socket should be orange Crit+Agility; every blue socket should be purple Stam + Agility. You helmut meta should be the Agility + 2% crit gem. Whey you want to gem something else DON'T; YOU WANT AGILITY. All you enchants should be Agility expecpt weapon which for a 2 hander should be Massacre. Get a real scope for your weapon i.e. the Heartseeker Scope.
As for gear, as pointed out above your 2 handed weapon is useless to you, hunter don't need Strength you want Agility, Agility and more Agility. Even Marrowstrike out of H ToC is far better. But the Orca Hunter's Harpoon is good too. Also, you have way too much hit. I would farm for a new ring and get rid of the PvP one and also, the PvP hit trinket can be replaced.
Now that we have a spec and gearing, you need a rotation; there's a addon called Watcher which can help you set a shot priority to follow; Also, there's another must have addon called ZugZug hunter which will let you take advantage of IMproved Tracking.
Rotation for Survival is Black Arrow, Explosive Shot, Aimed Shot, Serpent Sting, Steady Shot, then Steady Shot until Explosive Shot comes back up, then follow the priority.
In any event, good luck and check out Orcstar's guide on this site. Also, MaxDPS.com is a good site as is Femaledwarf.com.
Nightmare tear is the only blue gem you should ever use for your meta. In My personal opinion I don't think that blue sockets should be filled with a stamina agility gem. That is up to you though how you deal with that. If you truly want to know how your dps increases with each gem/enchant change you make I would recommend using
I can consistently easily get at least 6k in heroics, in VH I got up to 9k on the floating eye boss I think. With MM you get two rapid fires so with a few lucky procs and crits I can hit some high numbers.
I get between7k - 8k on festergut in 25 man ICC. I also get about 8500 on koralon in 25 voa. I have my hand mounted pyro rocket and silencing shot macro'd to my chimaera shot so they go off pretty often and I don't have to click extra shots.