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First Things first:
Opener
You start with your preperation while the pull timer counts down and have all ready to start the fight. For MNK this includes to charge up the first load of Chakra and reaching Courl Form.
Next is your Opener. The Opener is your start into the fight themself. In the Opener you race to get all your basic job mechanics runnung and time your buffs, pots and abilities to get a very high damage burst early in the fight.
For MNK the goal of the Opener is to get Greased Lightning III as fast as possible and use all your damage abilities (Forbidden Chakra, Elexier Field, Howling Fist and Steel Peaks) while they are influenced with all of your buffs (Blunt Resistence down, Inner Release, Riddle of Fire, Brotherhood).

Riddle of Fire
While it lengthens your weapon skill recast time it also grants huge damage up.
The damage up outweights the higher recast but comes into full advantage when combined with your damageing abilities, because abilities are going on cooldown and don't have a recast.
Nice siede effect of Riddle of Fire is its passive TP regen. While under the effect of Riddle of Fire you are using less or equal TP then you regen.

SkS and melding
Your main recast reducer is Greased Lightning. SkS has so less effect on this it's a shame and the bit you can attack more often mostly doesn't give you a benefit if you don't get to threshold you can fit in 1 more weapon skill within a specific buff duration.
Your main goal is to get as much Crit as you can, for even faster recharging of your Chakra outside of Brotherhood. The reason for this ist not the damage amplifier from the crits themselfs but from the more possible Forbidden Chakras.
If you have as much Crit as you can, even just +35 is better then +0, settle for Direct Hit. Direct Hit is at the moment the highest damage providing stat, for 160 points in Direct Hit you will get 1% more damage in average.
After Direct Hit the main contriibutor to Damage is Determination with 1% more damage for every 180 points.
Crit is the weakest at the moment but will raise over the expansion with higher item levels also it is your mechanic stat which boosts it to your focused secondary.
SkS is not really that great unless you get to specific threshold like 1 more weapon skill within your Riddle of Fire duration. But this damage gain is mostly underwhelming.

Clipping Damage over Time effects (DoTs)
This means you are reapplying your DoT (to) early. DoTs are counted in ticks every 3 seconds and every tick they damage for their DoT potency.
If you are reapplying your Dot to early you can miss some DoT ticks, which lowers the damage the DoT applying skill would do over the DoT duration.
Your goal for DoTs is to reapply them as late as possible while not letting them fall off to get to the max of its potencial damage.

Overlapping cooldowns
You should try to have as many of your cooldowns active simultaneously as possible to get your highest damage peaks.
Always use your cooldowns when they are comming off cooldown, except you know the boss will get untargetable or unreachable for you within a good bunch of the duration.

MNK Combos
MNK has another kind of Combo System then most other jobs.
They are not comboing skills, they are comboing their Forms: Opo-Opo to Raptor to Courl to Opo-Opo.
This makes it easy to adjust your combo depending on your needs.
The moment you hit the key for the skill and the skills comes off of cooldown the server processes your input and does the calculation for your damage including a snapshot of your positionals at that moment.
What you do while the animation goes off is irrelevant for the system.