Here's my TBS Disco clone with APM 2.6. All flight modes are working fine, still needs a little bit of tuning though. All parts are taken from my earlier F450 quad and reassembled. Thanks to Satya-Quadcopters.com (for the CNC frame job).

Specs:
APM 2.6 with Ublox 6M GPS Compass
APM Power module, 433MHzTelemetry, 5.8GHz 500mw FPV Tx, Mobius Wide angle
A2212/15T 930KV motors with 9x4.7" Nylon Carbon props, DYS 30A SimonK ESCs
Zippy 3S 2200mah Lipo

I have a query. I get a lot of Z-axis vibrations only (almost reaching -5 to -15) with 10x4.5 props but they are in control when using 9x4.7 props. Any recommendations from similar frame users for getting rid of these vibs? I have balanced props with tape.

First flight videos

What is the thickness of the material?

1.5mm

great build very stable..

Thanks!

great build,how much ₹₹ the frame cost you???

1K for Top & Bottom plates only..

Pitch gain should be a little more than the roll gain on this type of asymmetric frame. I used to experience video jello with 10" props but after moving to 9", I have eliminated all jello from the video. Basically I found that vibs reduce with increased motor rpm.

Is vibration in video your primary issue or vibration in FC?
How is althold/loiter working?
Do you have a log of the particular flight?
Are you retuning pid's when changing props?
Are you auto tuning?

If x/y axis are doing good then z axis variance must have something to do with baro(prop wash/ sunlight) or mag(EMI). Had vibration been the culprit, it should affect all the axis at the same time. Similar behavior can be observed with bad pid's but it would affect all the axis rather than just the Z. A log with all logging options enabled may help a lot.

Primary issue is vibration in FC. I have tried Alt Hold with 10" prop but the motors are pulsing, haven't tried Loiter.
Currently I'm using 9" props, Alt Hold & Loiter are fine, vibs are well under limits. The flight videos which I have posted earlier are done with 9x4.7 props.
I haven't done auto tune yet, will do this week.

Here is the log with 10" prop. Flew the quad indoors.

https://www.dropbox.com/s/ccq7daicq2shz1o/2015-03-14%2019-42-46.zip?dl=0

Good build there and thanks for the credit of the CNC

My suggestion is to go with 8 inch prop with 4S lipo you will get good performance.

A look at baro graph shows you have prop wash hitting the sensor. Its fluctuating at all times within a range of 0.5 to 1.5 meters rapidly which explains pulsating motors. Another evidence is that during the beginning of your flight, you are sitting at off 0 alt before take off, however as soon as your props spin up, alt drops to -4meters, then you begin flying at 1-2meters alt, however again while landing it drops to -4m right before landing and comes back to 0 when copter is landed and motors are not spinning. Thats a clear sign of baro getting disturbed due to the air that comes back from the floor.

This is how your baro graph looks,However


this is how it should look



It seems logging for everything isnt enabled, so cant figure out if magnetic interference is present. However your yaw is very erratic(image below) even when the input is unchanged(red line) which usually points out to mag interference.



Couple of other things which need attention are:
Power to FC is fluctuating a lot, crossing minimum threshold of .15v at times. I would never trust the power module that comes with APM. Its better to use a separate bec or ubec. Use PM only to check battery voltage and current consumption .

PID's are not upto the mark, if you observe roll vs desired roll, and similarly pitch. Most of the times your copter is overshooting while correcting after you request a change. But baro could be the culprit too.



Suggestion:

Take a look at baro as most of your flight woes seem related to it because, a sensitive baro would never let you get optimum PID. And you cant auto tune without althold. 
Dont cover the ABC lights on the board while covering baro, as light may get reflected to baro if you are using white foam specifically. Use dark coloured material. Just check the log of your 9" prop and see how baro readings look like & compare. We can move ahead to other issues once this is sorted, Infact you would only need an auto tune & everything should almost fall in place.