Obviously the COG should be centre for lateral placement and "as recommended" for longitudinal placement, but what happens if I move a component higher than usual - ie shifting the COG up ? Does this make the plane inherently more unstable? 

The reason I ask is that I am modifying my squadron (I have 3!!) of T28s and am thinking that I could do something clever with the canopy hatch - potentially by mounting the ardupilot (and possibly the RX) within in so I can swap in and out either different ardupilots quickly, or even swap in a "blanking template" into planes so I can just fly them manually (ie have a direct RX -> servo link in there). 

Feel free to redirect me to any appropriate web resources. I've read a lot about COG being too near the front or back but nothing about the height.