If my understanding is right: 3% with my setup is 2.67 sec a round VS 5% being 2.57. That is .1 sec difference per round. Again if math is right i am thinking roughly every 62.5 seconds if auto attaching with no WS or casting I would be losing 1 attack round? Is that right?
No, it's not. That delay difference is approximately a 4% increase in attack speed, which is the real number you should be looking at, and will also increase your WS frequency (ex with a 210/201 setup I'm getting about a 3.1% increase including WS delay). This number can be applied even if you don't gain a round because the final hit will occur sooner and thus killspeed still improves.
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The practical application I am trying to figure out would be variables like I would more than likely being casting at some point in those 62.5 seconds or WSing or the monster is already dead and I am moving to the next one.
Wait times actually favor Ninja +1 in the case of Kannagi because it reduces aftermath downtime via enhanced WS frequency. Kikoku doesn't really change either way.
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Other factors I am trying to look at are the +15 acc +20 attach on koga. Possibly that would help add extra points per swing helping to mitigate the lost round, or the acc could mean I dont miss a swing from just using af1+1.
Iga +2 is better than either if accuracy is relevant, even if Koga +2 is sufficient to cap hitrate.