Hi,
There have been issues in regards to GPS and compass in early versions of arducopter 4.0.
My understanding is that improvements have been made in 4.0.4 and further in 4.0.5.
Have had only limited flight time on later versions but did notice far less messages regarding “GPS-glitch” and compass related issues.
However, those latest versions are not supported by Navio and hence your coloured status LED won’t work. - But other than that everything works well in those versions.
Other info which might be helpful: Unhealthy GPS Signal?
In regards to Rpi2: Should certainly be powerful enough. if any doubt connect via SSH and simply enter “w” which will show processor load in a percentage value. - But this is only useful after about 15 minutes of up-time. Also would recommend checking this after a flight, not just on standby as usage / load values will be different in flight.
Hope this is of some help.