Hi, nice to see another Goodkind fan here

As Flashy pointed out, some features feel a little overpowered.

I want to share my attempt at the Mord-Sith which I posted around here few months ago:
https://drive.google.com/file/d/0Bzp...c5YU01OVE/view

For balancing the features there were a couple of things I was mindful about:
Making a class is much more difficult than making a path, so I designed the Mord-Sith as s Rogue archetype and compared it to the other 3 archetypes.
3rd level: You gain proficiency in 1 skill (for comparison Assassin gets 2 tools)
3rd level: You get Charm (for comparison so does Arcane Trickster, and can do it twice/day). With hours casting time it pretty much means once a day.
3rd level: You can create your own Agiel. It actually does less damage, but it can deal psychic damage, bypassing resistances. Also, at your DM's abjuration, it can count as magic item.
The extra damage comes from your Sneak Attack feature which is already (mostly) balanced.
9th level: You get an improved version of Counterspell, 4 levels earlier than Arcane Trickster (I'm not sure they get to choose Counterspell, but they get 3rd level spells at 13)
You can only perform it once per long rest.
13th level: You get Suggestion, which at this level is not that strong. The plus side is it lasts for several days and doesn't require concentration.
17th level: Your Counterspell upgrades to Spell Thief (same as Arcane Trickster), but you can do it 3 times between long rests.


As for your class, there are couple of observations you can work on:
Capture magic - Cha Mod / 2 rounded down is very little. Most other classes use Ability modifier or 1 + Ability modifier, always at least 1. If you want to use it less often just start with 1/day and give one or two more uses later, based on character level progression.
It is effectively a Counterspell at level 1 which is way too early. Wizards get it at level 5. Also countering Magic Missile and Power Word Kill has the same chance for success, which isn't very balanced.
Watchful Eye - +1 AC is probably ok. You can probably make it +2 AC and have it require concentration, like Shield of Faith. Does moving your ally prevent the damage? Also, as Flashy pointer out there are no encounter-based recharges in 5e. It's either short or long rest, with some high level features (Bardic Inspiration, Battle Master) giving you 1 use for free when you roll for Initiative and don't have any left.
Improved Weapons - gaining +1 magic weapon at 5 is probably fine. For +2 I'd say level 11th is a better milestone.
Improved Armor - I'm not sure many DM will be happy with this, I for one wouldn't be. Depends on your campaign but surely having a +2 weapon and +2 armor level 11 can easily put you before any other players. They also increase one ability to 19. It's like a rare armor and uncommon item in one. The abilities are also very beneficial to your class (Dex for AC/Saves, Con for HP/Saves, Cha for attack/damage/spell DC).
Pain Mastery - resistance itself is ok. Damage reduction at this level will be 9 or 10 (You *will* have 20 Charisma because all your skills require it, and you can get 19 Con from your armor). This means that a Fighter with a longsword (1d8+5) will do an average of NO damage against you (maybe 1-2 if they took the Duelist fighting style or have a magic weapon).
Dominating Capture gives your spellcasting opponent NO options for the first 3 rounds in combat (more if they fail the Stun save). Some CR 20 bosses have ONE 9th level spell.

I haven't checked the paths yet, but you can work on your base features first. Or, make it a path itself (rogue, fighter, paladin - Mord-Sith are kind of devoted).