How to go about setting up PX4 for a custom big hexarotor?

My team is building a custom hexarotor X-frame which is approximately 6ft in wingspan. We tested the electronics and comms on a smaller drone of the same frame type(S550). While we did not get any major issues with the S550 with respect to control, we got many with the bigger drone. On pitching it a bit in manual mode, it started oscillating and finally crashed.
On the bigger drone, we have the batteries on top of the thrust plane, which makes the CG point above the thrust plane.
How can we go about fixing these issues? We can try tuning the rate controllers but that would be very risky with a drone of that size.
I have added the flight log for the crash for reference.