All specs of Hunters are currently set back by a variety of negative bugs that are among the harder ones to detect. A lot of these exist on lots of other Trinity Core based servers, so I'll provide links from external sources wherever possible.
1) Pet GCD.
Pet GCD is currently 1.5 seconds instead of 1.25 seconds as it ought to be. This bug exists on all the other WotLK servers on this realm, and was confirmed on the Lordaeron bugtracker: https://www.warmane.com/bugtracker/report/8943
2) Steady Shot cast-time.
Steady Shot's cast-time isn't properly reduced by Haste. This is most easily confirmed by going BM, and seeing that even despite having points into Serpent's Swiftness, you aren't haste-capped (20% ranged haste from Serpent's Swiftness + 15% base ranged haste should automatically haste-cap BM Hunters even if they have 0 haste rating). This issue was confirmed and successfully fixed on Lordaeron: https://www.warmane.com/bugtracker/report/9170
3) Incorrect Crit Multipliers.
Several Hunter abilities aren't critting for as much as they should be. A lot of the information on this can be found here: https://github.com/TrinityCore/TrinityCore/issues/15099. I tested and confirmed this bug using Arcane Shot, and it was only critting for about 2.472x normal damage, when that figure should be 2.484x. This bug also likely applies to Chimera Shot, Chimera-Serpent, Kill Shot, and Auto Shot, although I wasn't able to test those due to not being able to buy a suitable bow (you need http://wotlk.openwow.com/item=15808 to properly test damage formulas since it has no damage range) to test it with.
This issue is caused by the meta-gem's bonus being applied into the calculation wrongly. The server is simply multiplying total crit damage by 3%. While this seems like the more intuitive way it ought to apply, it's not actually blizz-like.
4) Ammunition DPS normalization
This isn't a bug I was able to confirm (again, due to not having Fine Light Crossbow), but I strongly suspect it exists here due to the fact that several other Trinity Core-based private servers also have it, and because it's one of those bugs that next to no one realizes exists. This exists in Ragnaros/Deathwing, and possibly also Lordaeron (I haven't tested it on the latter yet).
The issue is that the DPS from your ammunition is normalized, as opposed to multiplied by your weapon's attack speed. If you have Iceblade Arrow and a 3.0 speed bow, the contribution from ammunition into the damage formulas of your spells should be the following: 3.0 x 91.5 = 274.5. Instead, the DPS of the arrows are normalized to a 2.8 speed, and so regardless of the speed of your bow, the contribution from ammo DPS with Iceblade Arrows is: 2.8 x 91.5 = 256.2.
Hunters using a bow faster than 2.8 speed are doing a bit too much damage, and Hunters using a bow slower than 2.8 speed are doing too little.
Evidence that ammunition DPS should not be normalized: http://forums.elitistjerks.com/forum...omment-1587827. It's also confirmed numerous times throughout that thread that it should indeed be that way, and this is also easily seen on Shandara's spreadsheet.