I've been having this issue for about a year now, and as of yet, haven't found a solution.
To start with, here is a video displaying the wagging yaw issue:
This yaw wagging only occurs with a top mounted yaw mechanism. I'm sure it's got everything to do with the mass of the yaw mechanism initially moving the tail in the opposite direction of where the controller wants it to go. Simply mounting the mechanism upside down 'solves' this issue since the mass of the mechanism helps move the tail in the direction the controller wants it to move.
I've tested this with Arducopter 2.9.1b and 3.1.2 firmware.
I've also swapped servos in order to reduce internal servo gear slop as much as possible.
When I used the KK2 board on this tricopter, it did not have this wagging issue.
The only downside to using a bottom mounted yaw mechanism is the much increased chance of prop strikes, especially when landing hard, or in rough terrain or braking for a landing. So I really hope this issue can be fixed or that someone can lead me in the right direction.
Want logs? Just tell me what you want logged and I'll let the tricopter wag for you.
Here's my previous request for help from last year: http://diydrones.com/forum/topics/arducopter-tricopter-firmware-oscillation-issues-with-top-mounted