Hello,
I currently have finished up on my TBS discovery long range build(around 600mm wheelbase).  I currently have a Chinese APM 2.6 but with the discontinuation of the and pilot project for APM boards I am looking about switching over to DJI for my control system.  However, I have been reading online that the Naza lite is not good for larger multi-copters and will cause some wobble.  Will it work for this larger setup or should I stick with the APM or would saving up for the Naza v2 be better for the larger quad?

I recomment the Naza V2 over the Naza Lite. It will be far more stable and will allow for other CAN Bus accessories in the future, such as a camera.