Hi Neil,
Congratulations, sounds like you've had a success.
I will say that the Raspberry Pi is probably a little under specced to be running Stars and Ekos locally which is why you may be seeing it as flakey. I'm still fairly new to the while INDI suite but I deliberated as to which way to run it and ended up grabbing an Intel Compute Stick to run Ekos and Stars at the mount on Lubuntu and remote control via VNC. The other option was to run a Pi as an INDI server only (Not KStars or Ekos) at the mount and the other applications on a Laptop, I just thought the Compute sticks were cute
For your setup and if you want to continue down the INDI path, the no cost (and easy, no need to roll your own) solution would be to install Virtualbox and run the INDI supplied Virtual machine
http://indilib.org/download/virtual-machines.html, whilst using the RPi to act as your INDI server providing the physical connection to your devices. Otherwise if you have an old Core 2 laptop laying around try Distro Astro, which comes bundled with Ekos, KStars, CdC, Stellarium, and a whole heap more and runs all of the applications quite well.
Happy to field any more questions if you need a hand.