Cyclone1,
You should be able to get things running reliably, especially with a semi-permanent antenna and GPS fit as this will allow you to optimise locations. I personally run my PAW from a UBlox GPS Mouse (available from the PilotAware site), and have had very few GPS problems throughout all the testing and flying I have done since starting to use it (which was well before PilotAware formally introduced them as an option).
I am however concerned at the recent reports of dropped connections. As I said above, changing to a GPS mouse or putting your GPS dongle onto a short extension lead to allow it to be sited in the clear, away from the main unit, should reduce the potential for screening of the WiFi dongle as well as moving the GPS away from any potential RF interference from the WiFi or the Raspberry Pi itself.
I will be very interested to hear whether this improves operation with your Runway HD.
p.s. if you do decide to go for an iPad (or mini), remember that you only need the cheaper WiFi only version as PilotAware supplies the necessary GPS data.
Regards
Peter